1. bsseq
  2. NAMESPACE
Browse code

Repair subsetByOverlaps() on hasGRanges derivatives

Also add overlapsAny() methods and improve granges() method for
hasGRanges derivatives.

Hervé Pagès authored on 20/05/2020 22:23:58
Showing 1 changed files
NAMESPACE
History View file @ 659aee2
... ... 
@@ -72,7 +72,7 @@ exportMethods("[", "show",
72 72 
               "dim", "nrow", "ncol",
73 73 
               "sampleNames", "sampleNames<-",
74 74 
               "pData", "pData<-",
75 
-              "findOverlaps", "subsetByOverlaps",
75 
+              "findOverlaps", "overlapsAny", "subsetByOverlaps",
76 76 
               "combine", "updateObject")
77 77
78 78 
 export("BSseq", "getMeth", "getCoverage", "getBSseq", "getStats",
Browse code

The rowsum() and colsum() generics are now defined in DelayedArray

Hervé Pagès authored on 31/01/2019 22:38:18
Showing 1 changed files
NAMESPACE
History View file @ d9114c7
... ... 
@@ -25,7 +25,7 @@ importFrom(graphics, "abline", "axis", "layout", "legend", "lines",
25 25 
 import(parallel)
26 26 
 importFrom(locfit, "locfit", "lp")
27 27 
 importFrom(DelayedMatrixStats, "rowSds", "rowVars", "colMeans2", "colSums2",
28 
-           "rowSums2", "rowMeans2", "rowAlls", "rowsum", "colsum")
28 
+           "rowSums2", "rowMeans2", "rowAlls")
29 29
30 30 
 importFrom(scales, "alpha")
31 31 
 importClassesFrom(Biobase, "AnnotatedDataFrame")
Browse code

fixing warnings

Kasper Daniel Hansen authored on 30/10/2018 00:57:46
Showing 1 changed files
NAMESPACE
History View file @ c4abf2a
... ... 
@@ -38,6 +38,8 @@ importMethodsFrom(GenomeInfoDb, "seqlengths", "seqlengths<-", "seqinfo",
38 38 
                   "seqlevels<-", "sortSeqlevels")
39 39 
 importFrom(GenomeInfoDb, "Seqinfo")
40 40 
 importFrom(gtools, "combinations")
41 
+importFrom(Rcpp, sourceCpp)
42 
+
41 43 
 # NOTE: data.table has some NAMESPACE clashes with functions in Bioconductor,
42 44 
 #       e.g., shift(). If new ones are discovered, add them to this list.
43 45 
 import(data.table, except = c(shift, first, second))
Browse code

Rename findCytosines as findLoci and document

Peter Hickey authored on 17/09/2018 11:02:52
Showing 1 changed files
NAMESPACE
History View file @ 57cc26c
... ... 
@@ -71,8 +71,7 @@ exportMethods("[", "show",
71 71 
               "sampleNames", "sampleNames<-",
72 72 
               "pData", "pData<-",
73 73 
               "findOverlaps", "subsetByOverlaps",
74 
-              "combine", "updateObject",
75 
-              "findCytosines")
74 
+              "combine", "updateObject")
76 75
77 76 
 export("BSseq", "getMeth", "getCoverage", "getBSseq", "getStats",
78 77 
        "collapseBSseq", "orderBSseq", "hasBeenSmoothed", "chrSelectBSseq",
... ... 
@@ -83,7 +82,7 @@ export("BSseq", "getMeth", "getCoverage", "getBSseq", "getStats",
83 82 
        "poissonGoodnessOfFit", "binomialGoodnessOfFit",
84 83 
        "data.frame2GRanges", "BSseqTstat",
85 84 
        "BSseqStat",
86 
-       "findCytosines")
85 
+       "findLoci")
87 86
88 87 
 S3method("print", "chisqGoodnessOfFit")
89 88 
 S3method("plot", "chisqGoodnessOfFit")
Browse code

Regenerate NAMESPACE

Peter Hickey authored on 21/08/2018 03:47:21
Showing 1 changed files
NAMESPACE
History View file @ 296c907
... ... 
@@ -25,7 +25,7 @@ importFrom(graphics, "abline", "axis", "layout", "legend", "lines",
25 25 
 import(parallel)
26 26 
 importFrom(locfit, "locfit", "lp")
27 27 
 importFrom(DelayedMatrixStats, "rowSds", "rowVars", "colMeans2", "colSums2",
28 
-           "rowSums2", "rowMeans2", "rowAlls", "rowGrid", "colGrid")
28 
+           "rowSums2", "rowMeans2", "rowAlls", "rowsum", "colsum")
29 29
30 30 
 importFrom(scales, "alpha")
31 31 
 importClassesFrom(Biobase, "AnnotatedDataFrame")
Browse code

Updates for recent changes

Peter Hickey authored on 20/07/2018 04:31:21
Showing 1 changed files
NAMESPACE
History View file @ 65e163c
... ... 
@@ -25,7 +25,7 @@ importFrom(graphics, "abline", "axis", "layout", "legend", "lines",
25 25 
 import(parallel)
26 26 
 importFrom(locfit, "locfit", "lp")
27 27 
 importFrom(DelayedMatrixStats, "rowSds", "rowVars", "colMeans2", "colSums2",
28 
-           "rowSums2", "rowMeans2", "rowAlls")
28 
+           "rowSums2", "rowMeans2", "rowAlls", "rowGrid", "colGrid")
29 29
30 30 
 importFrom(scales, "alpha")
31 31 
 importClassesFrom(Biobase, "AnnotatedDataFrame")
... ... 
@@ -46,7 +46,7 @@ importFrom(Biostrings, "DNAString", "vmatchPattern", "reverseComplement")
46 46 
 importFrom(utils, "read.delim")
47 47 
 importFrom(BSgenome, "vmatchPattern")
48 48 
 importFrom(tools, "file_path_as_absolute")
49 
-importFrom(R.utils, "isGzipped", "gunzip")
49 
+importFrom(R.utils, "isGzipped", "isBzipped", "gunzip", "bunzip2")
50 50
51 51 
 ##
52 52 
 ## Exporting
Browse code

Explicitly gunzip to tempfile()

Avoids error 'gzip: stdout: No space left on device' (https://github.com/Rdatatable/data.table/issues/717#issuecomment-226038307)

Peter Hickey authored on 04/07/2018 13:24:07
Showing 1 changed files
NAMESPACE
History View file @ 0656078
... ... 
@@ -46,7 +46,7 @@ importFrom(Biostrings, "DNAString", "vmatchPattern", "reverseComplement")
46 46 
 importFrom(utils, "read.delim")
47 47 
 importFrom(BSgenome, "vmatchPattern")
48 48 
 importFrom(tools, "file_path_as_absolute")
49 
-importFrom(R.utils, "isGzipped")
49 
+importFrom(R.utils, "isGzipped", "gunzip")
50 50
51 51 
 ##
52 52 
 ## Exporting
Browse code

Remove readr dependency

Found that `readr::read_tsv()` was painfully slow for large gzipped Bismark files (e.g., mCH loci).
Instead, now use:
- If file is gzipped and `gzip` is available at the command line, then use `data.table::fread()`.
- If file is gzipped and `gzip` is **not** available at the command line, then use `utils::read.table()`.
- If file is not gzipped (plain text) use `data.table::fread()`.

There are still some kinks to work out and tradeoffs to explore.

Peter Hickey authored on 04/07/2018 02:41:15
Showing 1 changed files
NAMESPACE
History View file @ 868a6f2
... ... 
@@ -42,11 +42,11 @@ importFrom(gtools, "combinations")
42 42 
 #       e.g., shift(). If new ones are discovered, add them to this list.
43 43 
 import(data.table, except = c(shift, first, second))
44 44 
 importFrom(permute, "shuffleSet", "how")
45 
-importFrom(readr, "cols", "cols_only", "col_character", "col_integer",
46 
-           "col_skip", "col_double", "col_factor", "read_tsv", "tokenizer_tsv")
47 45 
 importFrom(Biostrings, "DNAString", "vmatchPattern", "reverseComplement")
48 46 
 importFrom(utils, "read.delim")
49 47 
 importFrom(BSgenome, "vmatchPattern")
48 
+importFrom(tools, "file_path_as_absolute")
49 
+importFrom(R.utils, "isGzipped")
50 50
51 51 
 ##
52 52 
 ## Exporting
Browse code

Don't import stats::qnorm

Need to use the S4 generic `qrnom()` from DelayedArray. It's default method is `stats::qrnom()`, so it does the right thing.

Peter Hickey authored on 28/06/2018 23:33:16
Showing 1 changed files
NAMESPACE
History View file @ 1debd55
... ... 
@@ -18,7 +18,7 @@ importFrom(BiocGenerics, "anyDuplicated", "cbind", "colnames",
18 18 
            "strand", "strand<-", "union", "unique", "updateObject", "unstrand")
19 19 
 importFrom(stats, "approxfun", "fisher.test", "ppoints",
20 20 
            "predict", "preplot", "qchisq",
21 
-           "qnorm", "qqplot", "qunif", "cov2cor",
21 
+           "qqplot", "qunif", "cov2cor",
22 22 
            "setNames")
23 23 
 importFrom(graphics, "abline", "axis", "layout", "legend", "lines",
24 24 
            "mtext", "par", "plot", "points", "polygon", "rect", "rug", "text")
Browse code

Don't import stats::plogis

Need to use the S4 generic `plogis()` from DelayedArray. It's default method is `stats::plogis()`, so it does the right thing.

Peter Hickey authored on 28/06/2018 16:27:46
Showing 1 changed files
NAMESPACE
History View file @ 2420db8
... ... 
@@ -19,7 +19,7 @@ importFrom(BiocGenerics, "anyDuplicated", "cbind", "colnames",
19 19 
 importFrom(stats, "approxfun", "fisher.test", "ppoints",
20 20 
            "predict", "preplot", "qchisq",
21 21 
            "qnorm", "qqplot", "qunif", "cov2cor",
22 
-           "plogis", "setNames")
22 
+           "setNames")
23 23 
 importFrom(graphics, "abline", "axis", "layout", "legend", "lines",
24 24 
            "mtext", "par", "plot", "points", "polygon", "rect", "rug", "text")
25 25 
 import(parallel)
Browse code

Passing R CMD check locally without errors

- There are still warnings and notes
- And still more stuff to re-factor

Peter Hickey authored on 15/06/2018 00:48:26
Showing 1 changed files
NAMESPACE
History View file @ ca5bb6e
... ... 
@@ -46,6 +46,7 @@ importFrom(readr, "cols", "cols_only", "col_character", "col_integer",
46 46 
            "col_skip", "col_double", "col_factor", "read_tsv", "tokenizer_tsv")
47 47 
 importFrom(Biostrings, "DNAString", "vmatchPattern", "reverseComplement")
48 48 
 importFrom(utils, "read.delim")
49 
+importFrom(BSgenome, "vmatchPattern")
49 50
50 51 
 ##
51 52 
 ## Exporting
Browse code

Tweak DESCRIPTION and NAMESPACE

- HDF5Array and beachmat in Imports rather than Suggests

Peter Hickey authored on 14/06/2018 20:43:20
Showing 1 changed files
NAMESPACE
History View file @ 61dabc4
... ... 
@@ -3,6 +3,14 @@
3 3 
 ##
4 4
5 5 
 import(methods)
6 
+import(S4Vectors)
7 
+import(IRanges)
8 
+import(GenomicRanges)
9 
+import(SummarizedExperiment)
10 
+import(DelayedArray)
11 
+import(HDF5Array)
12 
+import(BiocParallel)
13 
+import(limma)
6 14 
 importFrom(BiocGenerics, "anyDuplicated", "cbind", "colnames",
7 15 
            "combine", "density", "intersect", "lapply", "ncol",
8 16 
            "nrow", "order", "paste", "pmax", "pmin", "rbind",
... ... 
@@ -18,9 +26,7 @@ import(parallel)
18 26 
 importFrom(locfit, "locfit", "lp")
19 27 
 importFrom(DelayedMatrixStats, "rowSds", "rowVars", "colMeans2", "colSums2",
20 28 
            "rowSums2", "rowMeans2", "rowAlls")
21 
-import(IRanges)
22 
-import(GenomicRanges)
23 
-import(SummarizedExperiment)
29 
+
24 30 
 importFrom(scales, "alpha")
25 31 
 importClassesFrom(Biobase, "AnnotatedDataFrame")
26 32 
 importMethodsFrom(Biobase, "annotatedDataFrameFrom",
... ... 
@@ -31,15 +37,11 @@ importMethodsFrom(GenomeInfoDb, "seqlengths", "seqlengths<-", "seqinfo",
31 37 
                   "seqinfo<-", "seqnames", "seqnames<-", "seqlevels",
32 38 
                   "seqlevels<-", "sortSeqlevels")
33 39 
 importFrom(GenomeInfoDb, "Seqinfo")
34 
-import(S4Vectors)
35 40 
 importFrom(gtools, "combinations")
36 41 
 # NOTE: data.table has some NAMESPACE clashes with functions in Bioconductor,
37 42 
 #       e.g., shift(). If new ones are discovered, add them to this list.
38 43 
 import(data.table, except = c(shift, first, second))
39 
-import(limma)
40 44 
 importFrom(permute, "shuffleSet", "how")
41 
-import(DelayedArray)
42 
-import(BiocParallel)
43 45 
 importFrom(readr, "cols", "cols_only", "col_character", "col_integer",
44 46 
            "col_skip", "col_double", "col_factor", "read_tsv", "tokenizer_tsv")
45 47 
 importFrom(Biostrings, "DNAString", "vmatchPattern", "reverseComplement")
Browse code

Quieten R CMD check

Peter Hickey authored on 14/06/2018 19:39:15
Showing 1 changed files
NAMESPACE
History View file @ 1823d04
... ... 
@@ -7,11 +7,11 @@ importFrom(BiocGenerics, "anyDuplicated", "cbind", "colnames",
7 7 
            "combine", "density", "intersect", "lapply", "ncol",
8 8 
            "nrow", "order", "paste", "pmax", "pmin", "rbind",
9 9 
            "Reduce", "rep.int", "rownames", "sapply", "setdiff",
10 
-           "strand", "strand<-", "union", "unique", "updateObject")
10 
+           "strand", "strand<-", "union", "unique", "updateObject", "unstrand")
11 11 
 importFrom(stats, "approxfun", "fisher.test", "ppoints",
12 12 
            "predict", "preplot", "qchisq",
13 13 
            "qnorm", "qqplot", "qunif", "cov2cor",
14 
-           "plogis")
14 
+           "plogis", "setNames")
15 15 
 importFrom(graphics, "abline", "axis", "layout", "legend", "lines",
16 16 
            "mtext", "par", "plot", "points", "polygon", "rect", "rug", "text")
17 17 
 import(parallel)
... ... 
@@ -27,15 +27,15 @@ importMethodsFrom(Biobase, "annotatedDataFrameFrom",
27 27 
                   "pData", "pData<-",
28 28 
                   "sampleNames", "sampleNames<-")
29 29 
 importFrom(Biobase, "validMsg")
30 
-importMethodsFrom(GenomeInfoDb, "seqlengths", "seqlengths<-", "seqinfo", "seqinfo<-",
31 
-                  "seqnames", "seqnames<-", "seqlevels", "seqlevels<-")
30 
+importMethodsFrom(GenomeInfoDb, "seqlengths", "seqlengths<-", "seqinfo",
31 
+                  "seqinfo<-", "seqnames", "seqnames<-", "seqlevels",
32 
+                  "seqlevels<-", "sortSeqlevels")
33 
+importFrom(GenomeInfoDb, "Seqinfo")
32 34 
 import(S4Vectors)
33 35 
 importFrom(gtools, "combinations")
34 
-# importFrom(data.table, "setnames", "setDT", "data.table", ":=", "setkey")
35 
-# TODO: More careful use of imports to avoid clashes (e.g., S4Vectors::shift()
36 
-#       and data.table::shift()).
37 
-import(data.table)
38 
-importFrom(R.utils, "isGzipped", "gunzip")
36 
+# NOTE: data.table has some NAMESPACE clashes with functions in Bioconductor,
37 
+#       e.g., shift(). If new ones are discovered, add them to this list.
38 
+import(data.table, except = c(shift, first, second))
39 39 
 import(limma)
40 40 
 importFrom(permute, "shuffleSet", "how")
41 41 
 import(DelayedArray)
... ... 
@@ -43,12 +43,12 @@ import(BiocParallel)
43 43 
 importFrom(readr, "cols", "cols_only", "col_character", "col_integer",
44 44 
            "col_skip", "col_double", "col_factor", "read_tsv", "tokenizer_tsv")
45 45 
 importFrom(Biostrings, "DNAString", "vmatchPattern", "reverseComplement")
46 
+importFrom(utils, "read.delim")
46 47
47 48 
 ##
48 49 
 ## Exporting
49 50 
 ##
50 51
51 
-
52 52 
 exportClasses("hasGRanges",
53 53 
               "BSseq",
54 54 
               "BSseqTstat",
Browse code

Improve `findCytosines()`

- Make generic with methods for _BSgenome_ and _DNAStringSet_ (e.g., a FASTA file imported with `rtracklayer::import()`)

Peter Hickey authored on 13/06/2018 14:17:09
Showing 1 changed files
NAMESPACE
History View file @ 5aa8515
... ... 
@@ -42,6 +42,8 @@ import(DelayedArray)
42 42 
 import(BiocParallel)
43 43 
 importFrom(readr, "cols", "cols_only", "col_character", "col_integer",
44 44 
            "col_skip", "col_double", "col_factor", "read_tsv", "tokenizer_tsv")
45 
+importFrom(Biostrings, "DNAString", "vmatchPattern", "reverseComplement")
46 
+
45 47 
 ##
46 48 
 ## Exporting
47 49 
 ##
... ... 
@@ -66,7 +68,8 @@ exportMethods("[", "show",
66 68 
               "sampleNames", "sampleNames<-",
67 69 
               "pData", "pData<-",
68 70 
               "findOverlaps", "subsetByOverlaps",
69 
-              "combine", "updateObject")
71 
+              "combine", "updateObject",
72 
+              "findCytosines")
70 73
71 74 
 export("BSseq", "getMeth", "getCoverage", "getBSseq", "getStats",
72 75 
        "collapseBSseq", "orderBSseq", "hasBeenSmoothed", "chrSelectBSseq",
... ... 
@@ -76,7 +79,8 @@ export("BSseq", "getMeth", "getCoverage", "getBSseq", "getStats",
76 79 
        "read.umtab", "read.umtab2", "read.bsmooth", "read.bismark",
77 80 
        "poissonGoodnessOfFit", "binomialGoodnessOfFit",
78 81 
        "data.frame2GRanges", "BSseqTstat",
79 
-       "BSseqStat")
82 
+       "BSseqStat",
83 
+       "findCytosines")
80 84
81 85 
 S3method("print", "chisqGoodnessOfFit")
82 86 
 S3method("plot", "chisqGoodnessOfFit")
Browse code

Split out R/read.bismark.R

Slightly formalise intermediate objects lociDT and BSseqDT.
Split these out into their own files.
Refine construction of 'gr' from Bismark files.

Peter Hickey authored on 31/05/2018 19:23:24
Showing 1 changed files
NAMESPACE
History View file @ 3c2dce4
... ... 
@@ -32,14 +32,16 @@ importMethodsFrom(GenomeInfoDb, "seqlengths", "seqlengths<-", "seqinfo", "seqinf
32 32 
 import(S4Vectors)
33 33 
 importFrom(gtools, "combinations")
34 34 
 # importFrom(data.table, "setnames", "setDT", "data.table", ":=", "setkey")
35 
+# TODO: More careful use of imports to avoid clashes (e.g., S4Vectors::shift()
36 
+#       and data.table::shift()).
35 37 
 import(data.table)
36 38 
 importFrom(R.utils, "isGzipped", "gunzip")
37 39 
 import(limma)
38 40 
 importFrom(permute, "shuffleSet", "how")
39 41 
 import(DelayedArray)
40 42 
 import(BiocParallel)
41 
-importFrom(readr, "count_fields", "cols_only", "col_character", "col_integer",
42 
-           "col_skip", "col_double", "read_tsv", "tokenizer_tsv")
43 
+importFrom(readr, "cols", "cols_only", "col_character", "col_integer",
44 
+           "col_skip", "col_double", "col_factor", "read_tsv", "tokenizer_tsv")
43 45 
 ##
44 46 
 ## Exporting
45 47 
 ##
Browse code

Merge branch 'refactor-read.bismark' into refactor

Peter Hickey authored on 29/05/2018 12:56:37
Showing 0 changed files
Browse code

Work in progress: refactoring bsseq

- BSseq objects can once again use ordinary matrix objects as assays.
- Reimplement `BSmooth()` more-or-less from scratch:
- Switch from 'parallel' to 'BiocParallel' for parallelization. This brings some notable improvements:
- Smoothed results can now be written directly to an on-disk realization backend by the worker. This dramatically reduces memory usage compared to previous versions of 'bsseq' that required all results be retained in-memory.
- Parallelization is now supported on Windows through the use of a 'SnowParam' object as the value of `BPPARAM`.
- Improved error handling makes it possible to gracefully resume `BSmooth()` jobs that encountered errors by re-doing only the necessary tasks.
- Detailed and extensive job logging facilities.
- Fix bug in `BSmooth()` with the `maxGap` parameter.
- Re-factor BSseq() constructor and add fast, internal .BSseq() constructor.
- Re-factor collapseBSseq() and combine(). Should be much more performant.
- Use beachmat to implement fast validity checking of 'M' and 'Cov' matrices.
- Resave BS.chr22 (supplied data) using integer for storage mode of assays to reduce size.
- Switch from RUnit to testthat. testthat has better integration with code coverage tools that help when refactoring.

Peter Hickey authored on 28/05/2018 23:42:18
Showing 1 changed files
NAMESPACE
History View file @ 866ab76
... ... 
@@ -17,7 +17,7 @@ importFrom(graphics, "abline", "axis", "layout", "legend", "lines",
17 17 
 import(parallel)
18 18 
 importFrom(locfit, "locfit", "lp")
19 19 
 importFrom(DelayedMatrixStats, "rowSds", "rowVars", "colMeans2", "colSums2",
20 
-           "rowSums2", "rowMeans2")
20 
+           "rowSums2", "rowMeans2", "rowAlls")
21 21 
 import(IRanges)
22 22 
 import(GenomicRanges)
23 23 
 import(SummarizedExperiment)
... ... 
@@ -35,10 +35,9 @@ importFrom(data.table, "fread", "setnames")
35 35 
 importFrom(R.utils, "isGzipped", "gunzip")
36 36 
 import(limma)
37 37 
 importFrom(permute, "shuffleSet", "how")
38 
-importClassesFrom(DelayedArray, "DelayedArray", "DelayedMatrix")
39 
-importFrom(DelayedArray, "DelayedArray", "plogis", "pmin2", "pmax2", "rowMaxs",
40 
-           "rowMins")
41 
-importClassesFrom(HDF5Array, "HDF5Array")
38 
+import(DelayedArray)
39 
+import(BiocParallel)
40 
+importFrom(Rcpp, "sourceCpp")
42 41
43 42 
 ##
44 43 
 ## Exporting
... ... 
@@ -86,3 +85,5 @@ S3method("plot", "BSseqTstat")
86 85
87 86 
 exportMethods("assays", "assayNames")
88 87
88 
+# C++ code registration
89 
+useDynLib(bsseq, .registration = TRUE, .fixes = "cxx_")
Browse code

Initial re-write of read.bismark()

Peter Hickey authored on 04/05/2018 18:31:03
Showing 1 changed files
NAMESPACE
History View file @ 3b038a9
... ... 
@@ -31,14 +31,18 @@ importMethodsFrom(GenomeInfoDb, "seqlengths", "seqlengths<-", "seqinfo", "seqinf
31 31 
                   "seqnames", "seqnames<-", "seqlevels", "seqlevels<-")
32 32 
 import(S4Vectors)
33 33 
 importFrom(gtools, "combinations")
34 
-importFrom(data.table, "fread", "setnames")
34 
+# importFrom(data.table, "setnames", "setDT", "data.table", ":=", "setkey")
35 
+import(data.table)
35 36 
 importFrom(R.utils, "isGzipped", "gunzip")
36 37 
 import(limma)
37 38 
 importFrom(permute, "shuffleSet", "how")
38 39 
 importClassesFrom(DelayedArray, "DelayedArray", "DelayedMatrix")
39 40 
 importFrom(DelayedArray, "DelayedArray", "plogis", "pmin2", "pmax2", "rowMaxs",
40 
-           "rowMins")
41 
+           "rowMins", "getRealizationBackend", "setRealizationBackend", "close",
42 
+           "RegularArrayGrid", "write_block_to_sink")
41 43 
 importClassesFrom(HDF5Array, "HDF5Array")
44 
+importFrom(readr, "count_fields", "cols_only", "col_character", "col_integer",
45 
+           "col_skip", "col_double", "read_tsv", "tokenizer_tsv")
42 46
43 47 
 ##
44 48 
 ## Exporting
Browse code

Another NAMESPACE/DESCRIPTION tweak

Peter Hickey authored on 24/04/2018 18:55:36
Showing 1 changed files
NAMESPACE
History View file @ 6995930
... ... 
@@ -38,6 +38,7 @@ importFrom(permute, "shuffleSet", "how")
38 38 
 importClassesFrom(DelayedArray, "DelayedArray", "DelayedMatrix")
39 39 
 importFrom(DelayedArray, "DelayedArray", "plogis", "pmin2", "pmax2", "rowMaxs",
40 40 
            "rowMins")
41 
+importClassesFrom(HDF5Array, "HDF5Array")
41 42
42 43 
 ##
43 44 
 ## Exporting
Browse code

Replace base/matrixStats/DelayedArray by DelayedMatrixStats

This is a straight find and replace of (col|row)(Sums|Means) with DelayedMatrixStats equivalents. Immediately, this is to work around an apparent bug in DelayedArray,rowSums-method (https://github.com/Bioconductor/DelayedArray/issues/16) but long term want to be using the optimised implementations in DelayedMatrixStat (e.g., using `cols` and `rows` args).

Peter Hickey authored on 24/04/2018 17:53:48
Showing 1 changed files
NAMESPACE
History View file @ 0275274
... ... 
@@ -16,8 +16,8 @@ importFrom(graphics, "abline", "axis", "layout", "legend", "lines",
16 16 
            "mtext", "par", "plot", "points", "polygon", "rect", "rug", "text")
17 17 
 import(parallel)
18 18 
 importFrom(locfit, "locfit", "lp")
19 
-importFrom(matrixStats, "rowSds", "rowVars", "rowMaxs", "rowMins", "colMeans2",
20 
-           "colSums2")
19 
+importFrom(DelayedMatrixStats, "rowSds", "rowVars", "colMeans2", "colSums2",
20 
+           "rowSums2", "rowMeans2")
21 21 
 import(IRanges)
22 22 
 import(GenomicRanges)
23 23 
 import(SummarizedExperiment)
... ... 
@@ -36,7 +36,8 @@ importFrom(R.utils, "isGzipped", "gunzip")
36 36 
 import(limma)
37 37 
 importFrom(permute, "shuffleSet", "how")
38 38 
 importClassesFrom(DelayedArray, "DelayedArray", "DelayedMatrix")
39 
-importFrom(DelayedArray, "DelayedArray", "plogis", "pmin2", "pmax2")
39 
+importFrom(DelayedArray, "DelayedArray", "plogis", "pmin2", "pmax2", "rowMaxs",
40 
+           "rowMins")
40 41
41 42 
 ##
42 43 
 ## Exporting
Browse code

Fix same performance regression in getCoverage() as in getMeth()

Peter Hickey authored on 03/07/2017 02:26:39
Showing 1 changed files
NAMESPACE
History View file @ 82aeb89
... ... 
@@ -16,7 +16,8 @@ importFrom(graphics, "abline", "axis", "layout", "legend", "lines",
16 16 
            "mtext", "par", "plot", "points", "polygon", "rect", "rug", "text")
17 17 
 import(parallel)
18 18 
 importFrom(locfit, "locfit", "lp")
19 
-importFrom(matrixStats, "rowSds", "rowVars", "rowMaxs", "rowMins", "colMeans2")
19 
+importFrom(matrixStats, "rowSds", "rowVars", "rowMaxs", "rowMins", "colMeans2",
20 
+           "colSums2")
20 21 
 import(IRanges)
21 22 
 import(GenomicRanges)
22 23 
 import(SummarizedExperiment)
Browse code

Fix performance regression in getMeth() [https://support.bioconductor.org/p/97611/]

Rather than 'split the overlaps' and then load in chunks of the data [as in the previous implementation of getMeth()], we load the methylation data in the regions into memory and split in memory. This is **much** more efficient but with the cost of loading more data into memory.

Peter Hickey authored on 03/07/2017 02:19:32
Showing 1 changed files
NAMESPACE
History View file @ 731e634
... ... 
@@ -16,7 +16,7 @@ importFrom(graphics, "abline", "axis", "layout", "legend", "lines",
16 16 
            "mtext", "par", "plot", "points", "polygon", "rect", "rug", "text")
17 17 
 import(parallel)
18 18 
 importFrom(locfit, "locfit", "lp")
19 
-importFrom(matrixStats, "rowSds", "rowVars", "rowMaxs", "rowMins")
19 
+importFrom(matrixStats, "rowSds", "rowVars", "rowMaxs", "rowMins", "colMeans2")
20 20 
 import(IRanges)
21 21 
 import(GenomicRanges)
22 22 
 import(SummarizedExperiment)
Browse code

Changes due to renaming in DelayedArray package

Peter Hickey authored on 11/04/2017 11:56:48
Showing 1 changed files
NAMESPACE
History View file @ 54cd877
... ... 
@@ -35,8 +35,7 @@ importFrom(R.utils, "isGzipped", "gunzip")
35 35 
 import(limma)
36 36 
 importFrom(permute, "shuffleSet", "how")
37 37 
 importClassesFrom(DelayedArray, "DelayedArray", "DelayedMatrix")
38 
-importFrom(DelayedArray, "DelayedArray", "plogis", "pmin2", "pmax2",
39 
-           "setRealizeBackend", "type")
38 
+importFrom(DelayedArray, "DelayedArray", "plogis", "pmin2", "pmax2")
40 39
41 40 
 ##
42 41 
 ## Exporting
Browse code

bsseq now uses DelayedMatrix objects from the DelayedArray package for all matrix-like data

Peter Hickey authored on 07/04/2017 17:42:29
Showing 1 changed files
NAMESPACE
History View file @ 95e9059
... ... 
@@ -10,7 +10,8 @@ importFrom(BiocGenerics, "anyDuplicated", "cbind", "colnames",
10 10 
            "strand", "strand<-", "union", "unique", "updateObject")
11 11 
 importFrom(stats, "approxfun", "fisher.test", "ppoints",
12 12 
            "predict", "preplot", "qchisq",
13 
-           "qnorm", "qqplot", "qunif", "cov2cor")
13 
+           "qnorm", "qqplot", "qunif", "cov2cor",
14 
+           "plogis")
14 15 
 importFrom(graphics, "abline", "axis", "layout", "legend", "lines",
15 16 
            "mtext", "par", "plot", "points", "polygon", "rect", "rug", "text")
16 17 
 import(parallel)
... ... 
@@ -33,6 +34,9 @@ importFrom(data.table, "fread", "setnames")
33 34 
 importFrom(R.utils, "isGzipped", "gunzip")
34 35 
 import(limma)
35 36 
 importFrom(permute, "shuffleSet", "how")
37 
+importClassesFrom(DelayedArray, "DelayedArray", "DelayedMatrix")
38 
+importFrom(DelayedArray, "DelayedArray", "plogis", "pmin2", "pmax2",
39 
+           "setRealizeBackend", "type")
36 40
37 41 
 ##
38 42 
 ## Exporting
Browse code

Experimental plotGeneTrack() Fiddle with par() options within plotAnnoTrack to try to make labels more legible when lots of annoTracks (and with long-ish names)

Peter Hickey authored on 11/05/2016 17:12:53
Showing 1 changed files
NAMESPACE
History View file @ 75b5aaa
... ... 
@@ -12,7 +12,7 @@ importFrom(stats, "approxfun", "fisher.test", "ppoints",
12 12 
            "predict", "preplot", "qchisq",
13 13 
            "qnorm", "qqplot", "qunif", "cov2cor")
14 14 
 importFrom(graphics, "abline", "axis", "layout", "legend", "lines",
15 
-           "mtext", "par", "plot", "points", "rect", "rug")
15 
+           "mtext", "par", "plot", "points", "polygon", "rect", "rug", "text")
16 16 
 import(parallel)
17 17 
 importFrom(locfit, "locfit", "lp")
18 18 
 importFrom(matrixStats, "rowSds", "rowVars", "rowMaxs", "rowMins")
Browse code

updates from master

From: Kasper Daniel Hansen <khansen@Tanngrisnir.local>

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bsseq@116910 bc3139a8-67e5-0310-9ffc-ced21a209358

khansen authored on 29/04/2016 04:18:31
Showing 1 changed files
NAMESPACE
History View file @ 70daf60
... ... 
@@ -68,7 +68,7 @@ export("BSseq", "getMeth", "getCoverage", "getBSseq", "getStats",
68 68 
        "read.umtab", "read.umtab2", "read.bsmooth", "read.bismark",
69 69 
        "poissonGoodnessOfFit", "binomialGoodnessOfFit",
70 70 
        "data.frame2GRanges", "BSseqTstat",
71 
-       "BSseqStat", "BSmooth.fstat", "smoothSds", "computeStat")
71 
+       "BSseqStat")
72 72
73 73 
 S3method("print", "chisqGoodnessOfFit")
74 74 
 S3method("plot", "chisqGoodnessOfFit")
Browse code

fixing merge

From: Kasper Daniel Hansen <kasperdanielhansen@gmail.com>

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bsseq@114621 bc3139a8-67e5-0310-9ffc-ced21a209358

khansen authored on 10/03/2016 17:06:33
Showing 1 changed files
NAMESPACE
History View file @ 3cfde51
... ... 
@@ -10,7 +10,7 @@ importFrom(BiocGenerics, "anyDuplicated", "cbind", "colnames",
10 10 
            "strand", "strand<-", "union", "unique", "updateObject")
11 11 
 importFrom(stats, "approxfun", "fisher.test", "ppoints",
12 12 
            "predict", "preplot", "qchisq",
13 
-           "qnorm", "qqplot", "qunif")
13 
+           "qnorm", "qqplot", "qunif", "cov2cor")
14 14 
 importFrom(graphics, "abline", "axis", "layout", "legend", "lines",
15 15 
            "mtext", "par", "plot", "points", "rect", "rug")
16 16 
 import(parallel)
Browse code

merge conflicts

From: Kasper Daniel Hansen <kasperdanielhansen@gmail.com>

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bsseq@114581 bc3139a8-67e5-0310-9ffc-ced21a209358

khansen authored on 10/03/2016 02:44:17
Showing 1 changed files
NAMESPACE
History View file @ 8657761
... ... 
@@ -15,7 +15,7 @@ importFrom(graphics, "abline", "axis", "layout", "legend", "lines",
15 15 
            "mtext", "par", "plot", "points", "rect", "rug")
16 16 
 import(parallel)
17 17 
 importFrom(locfit, "locfit", "lp")
18 
-importFrom(matrixStats, "rowSds", "rowVars")
18 
+importFrom(matrixStats, "rowSds", "rowVars", "rowMaxs", "rowMins")
19 19 
 import(IRanges)
20 20 
 import(GenomicRanges)
21 21 
 import(SummarizedExperiment)
... ... 
@@ -32,6 +32,7 @@ importFrom(gtools, "combinations")
32 32 
 importFrom(data.table, "fread", "setnames")
33 33 
 importFrom(R.utils, "isGzipped", "gunzip")
34 34 
 import(limma)
35 
+importFrom(permute, "shuffleSet", "how")
35 36
36 37 
 ##
37 38 
 ## Exporting
Browse code

fixed conflict

From: Kasper Daniel Hansen <kasperdanielhansen@gmail.com>

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bsseq@110074 bc3139a8-67e5-0310-9ffc-ced21a209358

khansen authored on 29/10/2015 19:12:43
Showing 1 changed files
NAMESPACE
History View file @ 65141d1
... ... 
@@ -31,6 +31,7 @@ import(S4Vectors)
31 31 
 importFrom(gtools, "combinations")
32 32 
 importFrom(data.table, "fread", "setnames")
33 33 
 importFrom(R.utils, "isGzipped", "gunzip")
34 
+import(limma)
34 35
35 36 
 ##
36 37 
 ## Exporting
... ... 
@@ -40,6 +41,7 @@ importFrom(R.utils, "isGzipped", "gunzip")
40 41 
 exportClasses("hasGRanges",
41 42 
               "BSseq",
42 43 
               "BSseqTstat",
44 
+              "BSseqStat",
43 45 
               "matrixOrNULL")
44 46
45 47 
 exportMethods("[", "show",
... ... 
@@ -64,7 +66,8 @@ export("BSseq", "getMeth", "getCoverage", "getBSseq", "getStats",
64 66 
        "plotRegion", "plotManyRegions",
65 67 
        "read.umtab", "read.umtab2", "read.bsmooth", "read.bismark",
66 68 
        "poissonGoodnessOfFit", "binomialGoodnessOfFit",
67 
-       "data.frame2GRanges", "BSseqTstat")
69 
+       "data.frame2GRanges", "BSseqTstat",
70 
+       "BSseqStat", "BSmooth.fstat", "smoothSds", "computeStat")
68 71
69 72 
 S3method("print", "chisqGoodnessOfFit")
70 73 
 S3method("plot", "chisqGoodnessOfFit")
Browse code

Commit made by the Bioconductor Git-SVN bridge.

Commit id: 21404fe8275c89f6f29231a680703827b0796ff9

Merge pull request #4 from PeteHaitch/master

Updates to read.bismark(), mostly documentation

Commit id: 6ba560784b0e6e6f2e8c40de72b4abf516dc14e3

Update tests and examples to use gzipped data. Ensure strand is kept for cytosineReport files if collapseStrand = FALSE.


Commit id: 41b003506ba63d0c7ec330c2ea0b826e0c1c5e9c

Remove Travis-CI. Not relevant at this juncture.


Commit id: 2fd84392d9f39409b6958f0ce0d77ea5e6476bee

Hardcode RVERSION in .travis.yml


Commit id: 127bc93e92cd065e94dbeac0001949e5c4138d91

Experimental Travis-CI support.


Commit id: a6fecb9692f9b72093d3e0e79cf39e325d63b1e9

Second pass at updating read.bismark() and docs. Updated DESCRIPTION in light of changes and added NEWS.rd entry.


Commit id: 5af9b047653567816174480a6f405e1d02f0a74b

First pass at re-write of read.bismark() and associated docs.



git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bsseq@106909 bc3139a8-67e5-0310-9ffc-ced21a209358

khansen authored on 30/07/2015 01:16:09
Showing 1 changed files
NAMESPACE
History View file @ 6b3c323
... ... 
@@ -30,6 +30,7 @@ importMethodsFrom(GenomeInfoDb, "seqlengths", "seqlengths<-", "seqinfo", "seqinf
30 30 
 import(S4Vectors)
31 31 
 importFrom(gtools, "combinations")
32 32 
 importFrom(data.table, "fread", "setnames")
33 
+importFrom(R.utils, "isGzipped", "gunzip")
33 34
34 35 
 ##
35 36 
 ## Exporting
... ... 
@@ -60,7 +61,7 @@ export("BSseq", "getMeth", "getCoverage", "getBSseq", "getStats",
60 61 
        "collapseBSseq", "orderBSseq", "hasBeenSmoothed", "chrSelectBSseq",
61 62 
        "BSmooth", "BSmooth.tstat", "dmrFinder", "fisherTests",
62 63 
        "combineList", "strandCollapse",
63 
-       "plotRegion", "plotManyRegions",
64 
+       "plotRegion", "plotManyRegions",
64 65 
        "read.umtab", "read.umtab2", "read.bsmooth", "read.bismark",
65 66 
        "poissonGoodnessOfFit", "binomialGoodnessOfFit",
66 67 
        "data.frame2GRanges", "BSseqTstat")
Browse code

Commit made by the Bioconductor Git-SVN bridge.

Commit id: 3e3c4a483adc9ba1e5d101a35f9a0fef41d2b78b

updated vignettes to use BiocStyle


Commit id: fe749c1df8a2a39ca6c4e1cc3b2358195f307631

updating read.bismark


Commit id: c50eb68c8e7f1be51af4ff411c95064849b52d15

Fixing Description; updating bsseq.Rnw to use BiocStyle


Commit id: f38a77394f0248aae1a6a4e27102610a53ca892e

resaved with compress=xz


Commit id: 2dcedd4fead08fe0af2a0afb7de2c89f4818b962

added Raw parsing of cytosine report files from Bismark



git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bsseq@104827 bc3139a8-67e5-0310-9ffc-ced21a209358

khansen authored on 11/06/2015 14:04:52
Showing 1 changed files
NAMESPACE
History View file @ 20c8b3b
... ... 
@@ -29,6 +29,7 @@ importMethodsFrom(GenomeInfoDb, "seqlengths", "seqlengths<-", "seqinfo", "seqinf
29 29 
                   "seqnames", "seqnames<-", "seqlevels", "seqlevels<-")
30 30 
 import(S4Vectors)
31 31 
 importFrom(gtools, "combinations")
32 
+importFrom(data.table, "fread", "setnames")
32 33
33 34 
 ##
34 35 
 ## Exporting
... ... 
@@ -58,7 +59,7 @@ exportMethods("[", "show",
58 59 
 export("BSseq", "getMeth", "getCoverage", "getBSseq", "getStats",
59 60 
        "collapseBSseq", "orderBSseq", "hasBeenSmoothed", "chrSelectBSseq",
60 61 
        "BSmooth", "BSmooth.tstat", "dmrFinder", "fisherTests",
61 
-       "combineList",
62 
+       "combineList", "strandCollapse",
62 63 
        "plotRegion", "plotManyRegions",
63 64 
        "read.umtab", "read.umtab2", "read.bsmooth", "read.bismark",
64 65 
        "poissonGoodnessOfFit", "binomialGoodnessOfFit",
Browse code

- BSseq class now extends new RangedSummarizedExperiment class from SummarizedExperiment package instead of "old" SummarizedExperiment class from GenomicRanges package. - Modify "updateObject" method for BSseq objects, and use it to update serialized object (BS.chr22.rda) contained in the package.

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bsseq@103650 bc3139a8-67e5-0310-9ffc-ced21a209358

hpages@fhcrc.org authored on 11/05/2015 21:38:11
Showing 1 changed files
NAMESPACE
History View file @ b2fd936
... ... 
@@ -18,6 +18,7 @@ importFrom(locfit, "locfit", "lp")
18 18 
 importFrom(matrixStats, "rowSds", "rowVars")
19 19 
 import(IRanges)
20 20 
 import(GenomicRanges)
21 
+import(SummarizedExperiment)
21 22 
 importFrom(scales, "alpha")
22 23 
 importClassesFrom(Biobase, "AnnotatedDataFrame")
23 24 
 importMethodsFrom(Biobase, "annotatedDataFrameFrom",
Browse code

Commit made by the Bioconductor Git-SVN bridge.

Commit id: 2155bb403810b2744c1ee1c364aa2fe6216a6671

bumped version


Commit id: f2df86b5e594d94aa0fd591152f9121554dfc47c

more work on permutations; now including unitTests


Commit id: 040af54e133c6fad141f3047a5b5a60772642b33

unit test for permutation matrix



git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bsseq@100731 bc3139a8-67e5-0310-9ffc-ced21a209358

khansen authored on 16/03/2015 19:57:19
Showing 1 changed files
NAMESPACE
History View file @ f351876
... ... 
@@ -27,6 +27,7 @@ importFrom(Biobase, "validMsg")
27 27 
 importMethodsFrom(GenomeInfoDb, "seqlengths", "seqlengths<-", "seqinfo", "seqinfo<-",
28 28 
                   "seqnames", "seqnames<-", "seqlevels", "seqlevels<-")
29 29 
 import(S4Vectors)
30 
+importFrom(gtools, "combinations")
30 31
31 32 
 ##
32 33 
 ## Exporting
Browse code

re-implement assayNames function as method

- on GenomicRanges::assayNames
- argument changed (from 'object' to 'x')


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bsseq@97133 bc3139a8-67e5-0310-9ffc-ced21a209358

mtmorgan@fhcrc.org authored on 26/11/2014 02:32:58
Showing 1 changed files
NAMESPACE
History View file @ e73ac2f
... ... 
@@ -70,6 +70,5 @@ S3method("plot", "BSseqTstat")
70 70
71 71 
 ## Fixes, to be removed
72 72
73 
-exportMethods("assays")
74 
-export("assayNames")
73 
+exportMethods("assays", "assayNames")
75 74
Browse code

Commit made by the Bioconductor Git-SVN bridge. Consists of 2 commits.

Commit information:

Commit id: 5ea7d2eb94ec7497dce8ddcfc971f324b38ded5f

bumped version

Committed by: Kasper Daniel Hansen
Author Name: Kasper Daniel Hansen
Commit date: 2014-10-28 11:42:23 -0400
Author date: 2014-10-28 11:42:23 -0400

Commit id: 137afbcd94987d9b7f6e9571282b1d6b927d8ea1

changed imports to support recent changes in the S4Vectors/GenomeInfoDb/GenomicRanges suite of packages

Committed by: Kasper Daniel Hansen
Author Name: Kasper Daniel Hansen
Commit date: 2014-10-28 11:41:56 -0400
Author date: 2014-10-28 11:41:56 -0400


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bsseq@96114 bc3139a8-67e5-0310-9ffc-ced21a209358

khansen authored on 28/10/2014 15:42:30
Showing 1 changed files
NAMESPACE
History View file @ cc27390
... ... 
@@ -8,14 +8,11 @@ importFrom(BiocGenerics, "anyDuplicated", "cbind", "colnames",
8 8 
            "nrow", "order", "paste", "pmax", "pmin", "rbind",
9 9 
            "Reduce", "rep.int", "rownames", "sapply", "setdiff",
10 10 
            "strand", "strand<-", "union", "unique", "updateObject")
11 
-
12 11 
 importFrom(stats, "approxfun", "fisher.test", "ppoints",
13 12 
            "predict", "preplot", "qchisq",
14 13 
            "qnorm", "qqplot", "qunif")
15 
-
16 14 
 importFrom(graphics, "abline", "axis", "layout", "legend", "lines",
17 15 
            "mtext", "par", "plot", "points", "rect", "rug")
18 
-
19 16 
 import(parallel)
20 17 
 importFrom(locfit, "locfit", "lp")
21 18 
 importFrom(matrixStats, "rowSds", "rowVars")
... ... 
@@ -27,6 +24,9 @@ importMethodsFrom(Biobase, "annotatedDataFrameFrom",
27 24 
                   "pData", "pData<-",
28 25 
                   "sampleNames", "sampleNames<-")
29 26 
 importFrom(Biobase, "validMsg")
27 
+importMethodsFrom(GenomeInfoDb, "seqlengths", "seqlengths<-", "seqinfo", "seqinfo<-",
28 
+                  "seqnames", "seqnames<-", "seqlevels", "seqlevels<-")
29 
+import(S4Vectors)
30 30
31 31 
 ##
32 32 
 ## Exporting
Browse code

typo fix for last commit

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bsseq@78231 bc3139a8-67e5-0310-9ffc-ced21a209358

khansen authored on 09/07/2013 20:13:30
Showing 1 changed files
NAMESPACE
History View file @ 47611c2
... ... 
@@ -70,6 +70,6 @@ S3method("plot", "BSseqTstat")
70 70
71 71 
 ## Fixes, to be removed
72 72
73 
-exportMethod("assays")
73 
+exportMethods("assays")
74 74 
 export("assayNames")
75 75
Browse code

temporary fixes to bsseq

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bsseq@78230 bc3139a8-67e5-0310-9ffc-ced21a209358

khansen authored on 09/07/2013 20:12:29
Showing 1 changed files
NAMESPACE
History View file @ a0f0863
... ... 
@@ -67,3 +67,9 @@ S3method("plot", "chisqGoodnessOfFit")
67 67 
 S3method("print", "summary.BSseqTstat")
68 68 
 S3method("summary", "BSseqTstat")
69 69 
 S3method("plot", "BSseqTstat")
70 
+
71 
+## Fixes, to be removed
72 
+
73 
+exportMethod("assays")
74 
+export("assayNames")
75 
+
Browse code

moved to a SummarizedExperiment backend for class 'BSseq'

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bsseq@78143 bc3139a8-67e5-0310-9ffc-ced21a209358

khansen authored on 06/07/2013 21:26:40
Showing 1 changed files
NAMESPACE
History View file @ 8e0ebd6
... ... 
@@ -7,7 +7,7 @@ importFrom(BiocGenerics, "anyDuplicated", "cbind", "colnames",
7 7 
            "combine", "density", "intersect", "lapply", "ncol",
8 8 
            "nrow", "order", "paste", "pmax", "pmin", "rbind",
9 9 
            "Reduce", "rep.int", "rownames", "sapply", "setdiff",
10 
-           "strand", "strand<-", "union", "unique")
10 
+           "strand", "strand<-", "union", "unique", "updateObject")
11 11
12 12 
 importFrom(stats, "approxfun", "fisher.test", "ppoints",
13 13 
            "predict", "preplot", "qchisq",
... ... 
@@ -25,9 +25,8 @@ importFrom(scales, "alpha")
25 25 
 importClassesFrom(Biobase, "AnnotatedDataFrame")
26 26 
 importMethodsFrom(Biobase, "annotatedDataFrameFrom",
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                   "pData", "pData<-",
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-                  "phenoData", "phenoData<-",
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                   "sampleNames", "sampleNames<-")
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-
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+importFrom(Biobase, "validMsg")
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 ##
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 ## Exporting
... ... 
@@ -50,10 +49,9 @@ exportMethods("[", "show",
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               "granges",
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               "dim", "nrow", "ncol",
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               "sampleNames", "sampleNames<-",
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-              "phenoData", "phenoData<-",
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               "pData", "pData<-",
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               "findOverlaps", "subsetByOverlaps",
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-              "combine")
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+              "combine", "updateObject")
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 export("BSseq", "getMeth", "getCoverage", "getBSseq", "getStats",
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        "collapseBSseq", "orderBSseq", "hasBeenSmoothed", "chrSelectBSseq",
Browse code

Added read.bismark function, along with documentation and example dataset for this function.

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bsseq@71341 bc3139a8-67e5-0310-9ffc-ced21a209358

p.hickey authored on 19/11/2012 22:53:38
Showing 1 changed files
NAMESPACE
History View file @ 4278410
... ... 
@@ -60,7 +60,7 @@ export("BSseq", "getMeth", "getCoverage", "getBSseq", "getStats",
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        "BSmooth", "BSmooth.tstat", "dmrFinder", "fisherTests",
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        "combineList",
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        "plotRegion", "plotManyRegions",
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-       "read.umtab", "read.umtab2", "read.bsmooth",
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+       "read.umtab", "read.umtab2", "read.bsmooth", "read.bismark",
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        "poissonGoodnessOfFit", "binomialGoodnessOfFit",
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        "data.frame2GRanges", "BSseqTstat")
66 66
Browse code

fix a latex error; bumping version

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bsseq@70595 bc3139a8-67e5-0310-9ffc-ced21a209358

khansen authored on 16/10/2012 19:35:29
Showing 1 changed files
NAMESPACE
History View file @ 4ef62d5
... ... 
@@ -58,6 +58,7 @@ exportMethods("[", "show",
58 58 
 export("BSseq", "getMeth", "getCoverage", "getBSseq", "getStats",
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        "collapseBSseq", "orderBSseq", "hasBeenSmoothed", "chrSelectBSseq",
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        "BSmooth", "BSmooth.tstat", "dmrFinder", "fisherTests",
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+       "combineList",
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        "plotRegion", "plotManyRegions",
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        "read.umtab", "read.umtab2", "read.bsmooth",
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        "poissonGoodnessOfFit", "binomialGoodnessOfFit",
Browse code

Adds bsseq and DBCiP to the repos.

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bsseq@67929 bc3139a8-67e5-0310-9ffc-ced21a209358

m.carlson authored on 20/07/2012 17:45:09
Showing 1 changed files
NAMESPACE
History View file @ 9f690ac
1 1 
new file mode 100644
... ... 
@@ -0,0 +1,70 @@
1 
+##
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+## Importing
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+##
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+
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+import(methods)
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+importFrom(BiocGenerics, "anyDuplicated", "cbind", "colnames",
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+           "combine", "density", "intersect", "lapply", "ncol",
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+           "nrow", "order", "paste", "pmax", "pmin", "rbind",
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+           "Reduce", "rep.int", "rownames", "sapply", "setdiff",
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+           "strand", "strand<-", "union", "unique")
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+
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+importFrom(stats, "approxfun", "fisher.test", "ppoints",
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+           "predict", "preplot", "qchisq",
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+           "qnorm", "qqplot", "qunif")
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+
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+importFrom(graphics, "abline", "axis", "layout", "legend", "lines",
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+           "mtext", "par", "plot", "points", "rect", "rug")
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+
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+import(parallel)
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+importFrom(locfit, "locfit", "lp")
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+importFrom(matrixStats, "rowSds", "rowVars")
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+import(IRanges)
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+import(GenomicRanges)
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+importFrom(scales, "alpha")
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+importClassesFrom(Biobase, "AnnotatedDataFrame")
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+importMethodsFrom(Biobase, "annotatedDataFrameFrom",
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+                  "pData", "pData<-",
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+                  "phenoData", "phenoData<-",
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+                  "sampleNames", "sampleNames<-")
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+
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+
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+##
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+## Exporting
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+##
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+
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+
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+exportClasses("hasGRanges",
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+              "BSseq",
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+              "BSseqTstat",
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+              "matrixOrNULL")
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+
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+exportMethods("[", "show",
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+              "seqnames", "seqnames<-",
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+              "seqlevels", "seqlevels<-",
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+              "seqlengths", "seqlengths<-",
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+              "start", "start<-",
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+              "end", "end<-",
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+              "width", "width<-",
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+              "strand", "strand<-",
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+              "granges",
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+              "dim", "nrow", "ncol",
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+              "sampleNames", "sampleNames<-",
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+              "phenoData", "phenoData<-",
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+              "pData", "pData<-",
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+              "findOverlaps", "subsetByOverlaps",
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+              "combine")
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+
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+export("BSseq", "getMeth", "getCoverage", "getBSseq", "getStats",
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+       "collapseBSseq", "orderBSseq", "hasBeenSmoothed", "chrSelectBSseq",
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+       "BSmooth", "BSmooth.tstat", "dmrFinder", "fisherTests",
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+       "plotRegion", "plotManyRegions",
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+       "read.umtab", "read.umtab2", "read.bsmooth",
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+       "poissonGoodnessOfFit", "binomialGoodnessOfFit",
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+       "data.frame2GRanges", "BSseqTstat")
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+
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+S3method("print", "chisqGoodnessOfFit")
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+S3method("plot", "chisqGoodnessOfFit")
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+S3method("print", "summary.BSseqTstat")
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+S3method("summary", "BSseqTstat")
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+S3method("plot", "BSseqTstat")