1. gmapR
  2. R
  3. GmapSnpDirectory-class.R
Browse code

elementLengths was renamed -> elementNROWS in S4Vectors (new name reflects TRUE semantic, old name will be deprecated soon)

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@113044 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 29/01/2016 01:22:03
Showing 1 changed files
R/GmapSnpDirectory-class.R
History View file @ d92a799
... ... 
@@ -31,7 +31,7 @@ setReplaceMethod("snps", c("GmapSnpDirectory", "character", "VCF"),
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                    iitFile <- file.path(iitPath, paste(name, "iit", sep = "."))
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                    alt <- values(gr)$ALT
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                    if (is(alt, "List")) {
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-                     gr <- rep(gr, elementLengths(alt))
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+                     gr <- rep(gr, elementNROWS(alt))
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                      alt <- unlist(alt)
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                    }
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                    ref <- values(gr)$REF
Browse code

renamed summarizeVariants to variantSummary the which in GsnapParam is now a GenomicRanges instead of a RangesList refactor the show method of BamTallyParam to rely on showAsCell

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@78525 bc3139a8-67e5-0310-9ffc-ced21a209358

Michael Lawrence authored on 15/07/2013 23:41:54
Showing 1 changed files
R/GmapSnpDirectory-class.R
History View file @ f3db568
... ... 
@@ -52,8 +52,8 @@ setReplaceMethod("snps", c("GmapSnpDirectory", "character", "character"),
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                    }
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                    param <- ScanVcfParam(fixed = "ALT", info = NA, geno = NA)
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-                   if (!missing(which)) # FIXME: waiting for vcfWhich<-
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-                     param@which <- as(which, "RangesList")
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+                   if (!missing(which))
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+                     vcfWhich(param) <- which
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                    snps(x, name = name, genome = genome, ...) <-
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                      readVcf(value, genome(genome), param)
Browse code

*drop passing of ... arg to method snps<- eventually dispatches on

*doc'ed ... arg to GmapSnps constructor

*added aliases for snps<- when first arg is a GmapGenomeDirectory

*test case for creating a GmapGenome via a DNAStringSet was
broken. Example sequence was too short for gmap_build to work


git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@69386 bc3139a8-67e5-0310-9ffc-ced21a209358

Cory Barr authored on 12/09/2012 22:29:42
Showing 1 changed files
R/GmapSnpDirectory-class.R
History View file @ 15766c6
... ... 
@@ -24,7 +24,7 @@ setMethod("length", "GmapSnpDirectory", function(x) {
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 setReplaceMethod("snps", c("GmapSnpDirectory", "character", "VCF"),
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                  function(x, name, genome = GmapGenome(genome(x)),
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-                          iitPath = tempdir(), ..., value)
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+                          iitPath = tempdir(), value)
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                  {
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                    gr <- rowData(value)
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                    values(gr) <- values(fixed(value))[c("REF", "ALT")]
Browse code

GmapSnpDirectory replace method now accepts name arg

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@69060 bc3139a8-67e5-0310-9ffc-ced21a209358

Cory Barr authored on 04/09/2012 22:50:45
Showing 1 changed files
R/GmapSnpDirectory-class.R
History View file @ 753b566
... ... 
@@ -22,7 +22,7 @@ setMethod("length", "GmapSnpDirectory", function(x) {
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   length(names(x))
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 })
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-setReplaceMethod("snps", c("GmapSnpDirectory", "VCF"),
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+setReplaceMethod("snps", c("GmapSnpDirectory", "character", "VCF"),
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                  function(x, name, genome = GmapGenome(genome(x)),
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                           iitPath = tempdir(), ..., value)
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                  {
... ... 
@@ -44,7 +44,7 @@ setReplaceMethod("snps", c("GmapSnpDirectory", "VCF"),
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                    x
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                  })
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-setReplaceMethod("snps", c("GmapSnpDirectory", "character"),
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+setReplaceMethod("snps", c("GmapSnpDirectory", "character", "character"),
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                  function(x, name, genome, which, ..., value)
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                  {
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                    if (missing(genome)) {
... ... 
@@ -54,6 +54,7 @@ setReplaceMethod("snps", c("GmapSnpDirectory", "character"),
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                    param <- ScanVcfParam(fixed = "ALT", info = NA, geno = NA)
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                    if (!missing(which)) # FIXME: waiting for vcfWhich<-
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                      param@which <- as(which, "RangesList")
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+
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                    snps(x, name = name, genome = genome, ...) <-
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                      readVcf(value, genome(genome), param)
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                    x
Browse code

handled case when GmapSnp obj is created with path to VCF, but no genome specified

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@68696 bc3139a8-67e5-0310-9ffc-ced21a209358

Cory Barr authored on 21/08/2012 23:49:18
Showing 1 changed files
R/GmapSnpDirectory-class.R
History View file @ 0664293
... ... 
@@ -47,6 +47,10 @@ setReplaceMethod("snps", c("GmapSnpDirectory", "VCF"),
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 setReplaceMethod("snps", c("GmapSnpDirectory", "character"),
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                  function(x, name, genome, which, ..., value)
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                  {
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+                   if (missing(genome)) {
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+                     stop("Please supply the \"genome\" argument")
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+                   }
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+
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                    param <- ScanVcfParam(fixed = "ALT", info = NA, geno = NA)
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                    if (!missing(which)) # FIXME: waiting for vcfWhich<-
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                      param@which <- as(which, "RangesList")
Browse code

renaming gmapR2 to gmapR: it lives again

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@68172 bc3139a8-67e5-0310-9ffc-ced21a209358

Michael Lawrence authored on 02/08/2012 22:24:24
Showing 1 changed files
R/GmapSnpDirectory-class.R
History View file @ b22faf0
1 1 
new file mode 100644
... ... 
@@ -0,0 +1,92 @@
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+### =========================================================================
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+### SnpDirectory class
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+### -------------------------------------------------------------------------
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+###
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+### Database of SNPs used by the GMAP suite.
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+###
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+
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+setClass("GmapSnpDirectory", representation(path = "character"))
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+
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+### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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+### Accessors
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+###
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+
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+setMethod("path", "GmapSnpDirectory", function(object) object@path)
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+
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+setMethod("names", "GmapSnpDirectory", function(x) {
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+  snp_files <- dir(path(x), ".*genomecomp\\.")
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+  sub("\\.genomecomp\\.", ":", snp_files)
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+})
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+
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+setMethod("length", "GmapSnpDirectory", function(x) {
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+  length(names(x))
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+})
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+
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+setReplaceMethod("snps", c("GmapSnpDirectory", "VCF"),
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+                 function(x, name, genome = GmapGenome(genome(x)),
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+                          iitPath = tempdir(), ..., value)
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+                 {
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+                   gr <- rowData(value)
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+                   values(gr) <- values(fixed(value))[c("REF", "ALT")]
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+                   iitFile <- file.path(iitPath, paste(name, "iit", sep = "."))
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+                   alt <- values(gr)$ALT
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+                   if (is(alt, "List")) {
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+                     gr <- rep(gr, elementLengths(alt))
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+                     alt <- unlist(alt)
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+                   }
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+                   ref <- values(gr)$REF
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+                   single <- nchar(alt) == 1L & nchar(ref) == 1L
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+                   change <- paste(ref[single], alt[single], sep = "")
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+                   gr <- gr[single]
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+                   values(gr) <- DataFrame(change)
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+                   export.iit(gr, iitFile)
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+                   snpindex(name, genome, path(x), iitFile)
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+                   x
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+                 })
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+
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+setReplaceMethod("snps", c("GmapSnpDirectory", "character"),
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+                 function(x, name, genome, which, ..., value)
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+                 {
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+                   param <- ScanVcfParam(fixed = "ALT", info = NA, geno = NA)
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+                   if (!missing(which)) # FIXME: waiting for vcfWhich<-
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+                     param@which <- as(which, "RangesList")
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+                   snps(x, name = name, genome = genome, ...) <-
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+                     readVcf(value, genome(genome), param)
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+                   x
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+                 })
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+
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+setMethod("[[<-", c("GmapSnpDirectory", value="ANY"),
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+          function(x, i, j, ..., value) {
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+            if (!missing(j))
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+              warning("argument 'j' ignored")
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+            snps(x, name = i, ...) <- value
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+            x
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+          })
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+
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+### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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+### Constructor
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+###
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+
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+GmapSnpDirectory <- function(path, create = FALSE) {
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+  if (is(path, "GmapGenome"))
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+    path <- path(path)
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+  if (!isSingleString(path))
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+    stop("'path' must be a single, non-NA string")
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+  if (!isTRUEorFALSE(create))
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+    stop("'create' must be TRUE or FALSE")
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+  if (create) {
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+    if (file.exists(path))
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+      message("NOTE: snp directory '", path, "' already exists, not recreating")
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+    else dir.create(path, recursive = TRUE)
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+  }
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+  new("GmapSnpDirectory", path = path)
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+}
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+
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+### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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+### Show
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+###
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+
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+setMethod("show", "GmapSnpDirectory", function(object) {
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+  cat("GmapSnpDirectory object\n", "path: ", path(object),
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+      "\nnames: ", names(object), "\n", sep = "")
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+})