1. crlmm
  2. R
  3. utils.R
Browse code

Added nopackage option for krlmm

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@117087 bc3139a8-67e5-0310-9ffc-ced21a209358

unknown authored on 03/05/2016 23:39:54
Showing 1 changed files
R/utils.R
History View file @ cbfc52e
... ... 
@@ -173,7 +173,8 @@ illuminaCdfNames <- function(){
173 173 
 	  "humanimmuno12v1b",       # Immuno chip 12
174 174 
 	  "humancytosnp12v2p1h",    # CytoSNP 12
175 175 
           "humanexome12v1p2a",      # Exome 12 v1.2 A
176 
-          "humanomniexpexome8v1p1b")
176 
+          "humanomniexpexome8v1p1b",
177 
+          "nopackage")
177 178 
 }
178 179
179 180 
 affyCdfNames <- function(){
Browse code

Added support for humanexome12v1.2a chip

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@94521 bc3139a8-67e5-0310-9ffc-ced21a209358

unknown authored on 25/09/2014 11:06:52
Showing 1 changed files
R/utils.R
History View file @ 1613e94
... ... 
@@ -172,6 +172,7 @@ illuminaCdfNames <- function(){
172 172 
 	  "humanomniexpress12v1b",  # Omni express 12
173 173 
 	  "humanimmuno12v1b",       # Immuno chip 12
174 174 
 	  "humancytosnp12v2p1h",    # CytoSNP 12
175 
+          "humanexome12v1p2a",      # Exome 12 v1.2 A
175 176 
           "humanomniexpexome8v1p1b")
176 177 
 }
177 178
Browse code

Changes to krlmm to avoid error that occurs in k-means clustering when all intensities are identical

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@88225 bc3139a8-67e5-0310-9ffc-ced21a209358

unknown authored on 01/04/2014 02:51:49
Showing 1 changed files
R/utils.R
History View file @ 3d8f487
... ... 
@@ -166,7 +166,8 @@ illuminaCdfNames <- function(){
166 166 
 	  "human1mduov3b",          # 1M Duo
167 167 
 	  "humanomni1quadv1b",      # Omni1 quad
168 168 
 	  "humanomni25quadv1b",     # Omni2.5 quad
169 
-	  "humanomni258v1a",        # Omni2.5 8
169 
+	  "humanomni258v1a",        # Omni2.5 8 v1 A
170 
+          "humanomni258v1p1b",      # Omni2.5 8 v1.1 B
170 171 
           "humanomni5quadv1b",      # Omni5 quad
171 172 
 	  "humanomniexpress12v1b",  # Omni express 12
172 173 
 	  "humanimmuno12v1b",       # Immuno chip 12
Browse code

merging from collab

* collab:
add warning in vignette about NAs with BafLrrSetList function
Added Human Omni Express Exome 8 v1.1b as a supported chip
updated version number of pacakge and man pages to reflect these changes
skeleton for krlmm capability added. genotype.Illumina() can now take and XY object as input
update copynumber.Rnw to use BafLrrSetList
updates to vignettes
update namespace

# Please enter a commit message to explain why this merge is necessary,
# especially if it merges an updated upstream into a topic branch.
#
# Lines starting with '#' will be ignored, and an empty message aborts
# the commit.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@79138 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 31/07/2013 01:37:34
Showing 1 changed files
R/utils.R
History View file @ 808cfec
... ... 
@@ -166,10 +166,12 @@ illuminaCdfNames <- function(){
166 166 
 	  "human1mduov3b",          # 1M Duo
167 167 
 	  "humanomni1quadv1b",      # Omni1 quad
168 168 
 	  "humanomni25quadv1b",     # Omni2.5 quad
169 
-	  "humanomni258v1a",        # Omni2.5 8 sample
169 
+	  "humanomni258v1a",        # Omni2.5 8
170 
+          "humanomni5quadv1b",      # Omni5 quad
170 171 
 	  "humanomniexpress12v1b",  # Omni express 12
171 172 
 	  "humanimmuno12v1b",       # Immuno chip 12
172 
-	  "humancytosnp12v2p1h")    # CytoSNP 12
173 
+	  "humancytosnp12v2p1h",    # CytoSNP 12
174 
+          "humanomniexpexome8v1p1b")
173 175 
 }
174 176
175 177 
 affyCdfNames <- function(){
Browse code

merge with collab branch containing fix for dqrls and bug-fix for computeRBaf that can misalign sample index with batch index (when batch is not in alphabetical order)

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@71295 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 17/11/2012 15:24:46
Showing 1 changed files
R/utils.R
History View file @ a3b625d
... ... 
@@ -14,8 +14,11 @@ getCrlmmAnnotationName <- function(x){
14 14 
 	paste(tolower(gsub("_", "", x)), "Crlmm", sep="")
15 15 
 }
16 16
17 
+## medianSummaries <- function(mat, grps)
18 
+##   .Call("R_subColSummarize_median", mat, grps, PACKAGE = "preprocessCore")
19 
+
17 20 
 medianSummaries <- function(mat, grps)
18 
-  .Call("R_subColSummarize_median", mat, grps, PACKAGE = "preprocessCore")
21 
+.Call("subColSummarizeMedianPP", mat, grps)
19 22
20 23 
 intMedianSummaries <- function(mat, grps)
21 24 
   as.integer(medianSummaries(mat, grps))
Browse code

Merge branch 'collab'

* collab:
Update CNSet objects in data/ with datadir slot and protocolData(object)$filename
update cnrmaAffy. processCEL2 located inside cnrmaAffy function. Uses lexical scope.
Change API for genotypeAffy -- remove mixtureParams argument. Update call to genotypeAffy in genotype function
snprmaAffy no longer initializes mixtureParams object, but accesses this information from the cnSet
constructAffyCNSet initializes mixtureParams slot of the appropriate dimensions
updated cnrmaAffy. Removed cnrma2, cnrma. cnrmaAffy uses lexical scope
Fix bug in crlmmGT2 caused by unequal batch sizes
Moved rsprocessCel inside of snprmaAffy for lexical scope. Moved imputeGender inside crlmmGT2 for lexical scope
Revert imputeGender to original approach for crlmm. Splitting samples across nodes does not work well if there are not a lot of samples in the individual nodes. Probably better to use fewer markers on chr X when large number of samples are processed
contains old process1 call
change gender <- unlist(gender) to gender <- unlist(genderList)
v1.15.15 Fix memory leak in imputeGender step by running this function in sample batches of size ocSamples(). Use lexical scope in calling process1 function in crlmmGT2.
set default values in summarizeNps
depends on v 1.19.39 of oligoClasses
v1.15.14: Export constructAffyCNSet. Used datadir slot in CNSet object added to v 1.19.39 of oligoClasses
update getFeatureData for use with annotation package that contains a number of SNPs not necessarily included in the genotyping. These additional snps are removed when constructing the featureData in constructAffy

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@67826 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 19/07/2012 03:57:08
Showing 1 changed files
R/utils.R
History View file @ e31c779
... ... 
@@ -11,7 +11,7 @@ changeToCrlmmAnnotationName <- function(x){
11 11 
 }
12 12
13 13 
 getCrlmmAnnotationName <- function(x){
14 
-  paste(tolower(gsub("_", "", x)), "Crlmm", sep="")
14 
+	paste(tolower(gsub("_", "", x)), "Crlmm", sep="")
15 15 
 }
16 16
17 17 
 medianSummaries <- function(mat, grps)
Browse code

Merge branch 'collab'

* collab: (34 commits)
revert change to IlluminaPreprocessCN
fix bug in isValidCdfName
print warning when all features in a batch of probes are flagged, but allow processing to continue
add utility cleancdfnames
Add validCdfNames.Rd
export validCdfNames
imputeGender fix when chromosome Y not available
Use splitIndicesByLength(index, ocSamples/getDoParWorkers())
Can not allocate vector of size XG with genotype.Illumina. Use splitIndicesByNode() only if the length of the list is greater than the split from splitIndicesByLength(). Otherwise, split by length using ocSamples()
update .gitignore
Add make.unique for sampleSheet$Sample_ID in readIdatFiles
bug in description
ensure sample ids stored in samplesheet are unique when constructing cnSet object
update oligoClasses dependency
update unit test for genotype.Illumina
revert change in constructInf call from genotype.Illumina
Update genotype.Rd
edit ACN function
1.15.6 use make.unique(basename(arrayNames)) to allow processing of Illumina samples with duplicated barcodes
check that sample identifies are unique in crlmm function
...

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@67435 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 08/07/2012 19:00:03
Showing 1 changed files
R/utils.R
History View file @ 063b3d1
... ... 
@@ -152,30 +152,39 @@ celDates <- function(celfiles){
152 152 
 	return(celdts)
153 153 
 }
154 154
155 
-validCdfNames <- function(){
155 
+illuminaCdfNames <- function(){
156 
+	c("human1mv1c",# 1M
157 
+	  "human370v1c",            # 370CNV
158 
+	  "human650v3a",            # 650Y
159 
+	  "human610quadv1b",        # 610 quad
160 
+	  "human660quadv1a",        # 660 quad
161 
+	  "human370quadv3c",        # 370CNV quad
162 
+	  "human550v3b",            # 550K
163 
+	  "human1mduov3b",          # 1M Duo
164 
+	  "humanomni1quadv1b",      # Omni1 quad
165 
+	  "humanomni25quadv1b",     # Omni2.5 quad
166 
+	  "humanomni258v1a",        # Omni2.5 8 sample
167 
+	  "humanomniexpress12v1b",  # Omni express 12
168 
+	  "humanimmuno12v1b",       # Immuno chip 12
169 
+	  "humancytosnp12v2p1h")    # CytoSNP 12
170 
+}
171 
+
172 
+affyCdfNames <- function(){
156 173 
 	c("genomewidesnp6",
157 
-	  "genomewidesnp5",
158 
-	  "human370v1c",
159 
-	  "human370quadv3c",
160 
-	  "human550v3b",
161 
-	  "human650v3a",
162 
-	  "human610quadv1b",
163 
-	  "human660quadv1a",
164 
-	  "human1mduov3b",
165 
-	  "humanomni1quadv1b",
166 
-          "humanomniexpress12v1b",
167 
-	  "humanomni25quadv1b",
168 
-          "humanimmuno12v1b",
169 
-          "humancytosnp12v2p1h")
174 
+	  "genomewidesnp5")
170 175 
 }
176 
+
177 
+validCdfNames <- function(){
178 
+	c(affyCdfNames(),
179 
+	  illuminaCdfNames())
180 
+}
181 
+
182 
+cleancdfname <- function(x) strsplit(x, "Crlmm")[[1]][[1]]
183 
+
171 184 
 isValidCdfName <- function(cdfName){
172 185 
 	chipList <- validCdfNames()
173 
-	result <- cdfName %in% chipList
174 
-	if(!(result)){
175 
-		warning("cdfName must be one of the following: ",
176 
-			chipList)
177 
-	}
178 
-	return(result)
186 
+	match.arg(cleancdfname(cdfName), chipList)
187 
+	return(TRUE)
179 188 
 }
180 189
181 190 
 isPackageLoaded <- function(pkg){
Browse code

Merge branch 'collab'

* collab:
bump version
made cnSetExample smaller. Fix notes
Trying to revert bad commit
remove cn-functions. update description
comment most of cn-functions.r
Resaved rdas
update data/cnSetExample.rda and data/cnSetExample2.rda
bump version
coercion method from CNSet to oligoSnpSet makes integer matrices of BAFs and lrr's
import ff_or_matrix from oligoClasses. bump dependency on oligoClasses version. Use library(oligoClasses) in some of the crlmm examples.
Cleaning pkg loading process: work still required
move Biobase and methods to imports

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@64324 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 23/03/2012 03:34:50
Showing 1 changed files
R/utils.R
History View file @ ad3cc70
... ... 
@@ -214,7 +214,7 @@ setMethod("annotatedDataFrameFrom", "ffdf", Biobase:::annotatedDataFrameFromMatr
214 214
215 215 
 ## Document this...
216 216 
 getBAF <- function(theta, canonicalTheta)
217 
-    .Call('normalizeBAF', theta, ct)
217 
+    .Call('normalizeBAF', theta, canonicalTheta)
218 218
219 219
220 220 
 validCEL <- function(celfiles){
Browse code

Merge branch 'mymac'

* mymac:
add AffyGW.pdf
update vignettes in inst/scripts
Change argument of validCEL to celfiles
Update constructInf to accommodate GenomeDataFrame class for featureData
bump version to 1.13.7
Add doRUnit.R
Add celfile-utils.Rd
Streamlne some of the Rd files
add validCEL function that checks whether all celfiles can be read
getFeatureData returns GenomeAnnotatedDataFrame
Remove imports from methods. Remove pdf of illumina_copynumber.pdf (large file) and copynumber.pdf
getFeatureDAta returns GenomeAnnotatedDataFrame
Remove separate vignette for copy number in inst/scripts. Include copynumber section in both affy and illumina pipelines.
update documentation files for genotype.Illumina, preprocessInf, and genotypeInf (cdfName added as argument. Indicate that 'batch' should be a character string)
pass cdfName to genotypeInf and preprocessInf
add unitTests and cn-functions for 'simple usage'
Combine AffyPreprocess and copynumber. Combine IlluminaPreprocess and copynumber
remove depency on ff to allow installation on my mac

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@62108 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 17/01/2012 19:13:44
Showing 1 changed files
R/utils.R
History View file @ 7c0c9ac
... ... 
@@ -216,3 +216,14 @@ setMethod("annotatedDataFrameFrom", "ffdf", Biobase:::annotatedDataFrameFromMatr
216 216 
 getBAF <- function(theta, canonicalTheta)
217 217 
     .Call('normalizeBAF', theta, ct)
218 218
219 
+
220 
+validCEL <- function(celfiles){
221 
+	for(i in seq_along(celfiles)){
222 
+		res <- tryCatch(read.celfile(celfiles[i], intensity.means.only=TRUE), error=function(e) NULL)
223 
+		if(is.null(res)) {
224 
+			msg <- message("Problem reading ", celfiles[i])
225 
+			stop(msg)
226 
+		}
227 
+	}
228 
+	return("Successfully read all cel files")
229 
+}
Browse code

adding normalizeBAF

Adding normalizeBAF(theta, canonicalTheta), implemented in C.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@58753 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 04/10/2011 16:11:12
Showing 1 changed files
R/utils.R
History View file @ 09f0b30
... ... 
@@ -216,4 +216,3 @@ setMethod("annotatedDataFrameFrom", "ffdf", Biobase:::annotatedDataFrameFromMatr
216 216 
 getBAF <- function(theta, canonicalTheta)
217 217 
     .Call('normalizeBAF', theta, ct)
218 218
219 
-
Browse code

crlmm on github

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@58751 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 04/10/2011 16:11:02
Showing 1 changed files
R/utils.R
History View file @ af08b5d
... ... 
@@ -215,3 +215,5 @@ setMethod("annotatedDataFrameFrom", "ffdf", Biobase:::annotatedDataFrameFromMatr
215 215 
 ## Document this...
216 216 
 getBAF <- function(theta, canonicalTheta)
217 217 
     .Call('normalizeBAF', theta, ct)
218 
+
219 
+
Browse code

bringing changes from GitHub; from now on, keeping code on BioC servers

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@58710 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 03/10/2011 18:12:55
Showing 1 changed files
R/utils.R
History View file @ b6f0c38
... ... 
@@ -211,3 +211,7 @@ loadObject <- function(filename, load.it){
211 211
212 212 
 setMethod("annotatedDataFrameFrom", "ff_matrix", Biobase:::annotatedDataFrameFromMatrix)
213 213 
 setMethod("annotatedDataFrameFrom", "ffdf", Biobase:::annotatedDataFrameFromMatrix)
214 
+
215 
+## Document this...
216 
+getBAF <- function(theta, canonicalTheta)
217 
+    .Call('normalizeBAF', theta, ct)
Browse code

Added 'humancytosnp12v2p1h' as a new chip type for Illumina arrays

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@57404 bc3139a8-67e5-0310-9ffc-ced21a209358

unknown authored on 12/08/2011 06:42:13
Showing 1 changed files
R/utils.R
History View file @ 01aea5e
... ... 
@@ -165,7 +165,8 @@ validCdfNames <- function(){
165 165 
 	  "humanomni1quadv1b",
166 166 
           "humanomniexpress12v1b",
167 167 
 	  "humanomni25quadv1b",
168 
-          "humanimmuno12v1b")
168 
+          "humanimmuno12v1b",
169 
+          "humancytosnp12v2p1h")
169 170 
 }
170 171 
 isValidCdfName <- function(cdfName){
171 172 
 	chipList <- validCdfNames()
Browse code

Check batch early in genotype function. Add genotypeRS function to genotype Illumina data. Fix stop message in getVarInEnv -- do not try to print envir.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@53853 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 18/03/2011 01:57:30
Showing 1 changed files
R/utils.R
History View file @ cfa9fbb
... ... 
@@ -33,7 +33,7 @@ isLoaded <- function(dataset, environ=.crlmmPkgEnv)
33 33
34 34 
 getVarInEnv <- function(dataset, environ=.crlmmPkgEnv){
35 35 
 	if (!isLoaded(dataset, environ=environ))
36 
-		stop("Variable ", dataset, " not found in ", environ)
36 
+		stop("Variable ", dataset, " not found in supplied environment")
37 37 
 	environ[[dataset]]
38 38 
 }
39 39
Browse code

commit after bioc rebase

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@52859 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 16/02/2011 16:19:11
Showing 1 changed files
R/utils.R
History View file @ 453e688
... ... 
@@ -32,8 +32,8 @@ isLoaded <- function(dataset, environ=.crlmmPkgEnv)
32 32 
 	exists(dataset, envir=environ)
33 33
34 34 
 getVarInEnv <- function(dataset, environ=.crlmmPkgEnv){
35 
-	if (!isLoaded(dataset))
36 
-		stop("Variable ", dataset, " not found in .crlmmPkgEnv")
35 
+	if (!isLoaded(dataset, environ=environ))
36 
+		stop("Variable ", dataset, " not found in ", environ)
37 37 
 	environ[[dataset]]
38 38 
 }
39 39
... ... 
@@ -168,12 +168,19 @@ validCdfNames <- function(){
168 168 
           "humanimmuno12v1b")
169 169 
 }
170 170 
 isValidCdfName <- function(cdfName){
171 
-    stopifnot(is.character(cdfName))
172 
-    result <- cdfName %in% validCdfNames()
173 
-    if (!result)
174 
-        warning("cdfName must be one of the following: ",
175 
-                chipList)
176 
-    return(result)
171 
+	chipList <- validCdfNames()
172 
+	result <- cdfName %in% chipList
173 
+	if(!(result)){
174 
+		warning("cdfName must be one of the following: ",
175 
+			chipList)
176 
+	}
177 
+	return(result)
178 
+}
179 
+
180 
+isPackageLoaded <- function(pkg){
181 
+	stopifnot(is.character(pkg))
182 
+	pkg <- paste("package:", pkg, sep="")
183 
+	pkg %in% search()
177 184 
 }
178 185
179 186 
 paramNames <- function(){
Browse code

Cleaning up... importing isPackageLoaded() from oligoClasses

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@51994 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 20/01/2011 18:33:39
Showing 1 changed files
R/utils.R
History View file @ 4c729c3
... ... 
@@ -94,9 +94,6 @@ list2SnpSet <- function(x, returnParams=FALSE){
94 94 
                           "Center AA", "Center AB", "Center BB",
95 95 
                           "Scale AA", "Scale AB", "Scale BB",
96 96 
                           "N AA", "N AB", "N BB"),
97 
-#                          "Shift in parameters AA",
98 
-#                          "Shift in parameters AB",
99 
-#                          "Shift in parameters BB"),
100 97 
                         row.names=c(
101 98 
                           "SNPQC",
102 99 
                           "cAA", "cAB", "cBB",
... ... 
@@ -142,8 +139,7 @@ loader <- function(theFile, envir, pkgname){
142 139
143 140 
 celDates <- function(celfiles){
144 141 
 	if(!all(file.exists(celfiles))) stop("1 or more cel file does not exist")
145 
-	celdates <- vector("character", length(celfiles))
146 
-	celtimes <- vector("character", length(celfiles))
142 
+	celdates <- celtimes <- vector("character", length(celfiles))
147 143 
 	for(i in seq(along=celfiles)){
148 144 
 		if(i %% 100 == 0) cat(".")
149 145 
 		tmp <- read.celfile.header(celfiles[i], info="full")$DatHeader
... ... 
@@ -172,19 +168,12 @@ validCdfNames <- function(){
172 168 
           "humanimmuno12v1b")
173 169 
 }
174 170 
 isValidCdfName <- function(cdfName){
175 
-	chipList <- validCdfNames()
176 
-	result <- cdfName %in% chipList
177 
-	if(!(result)){
178 
-		warning("cdfName must be one of the following: ",
179 
-			chipList)
180 
-	}
181 
-	return(result)
182 
-}
183 
-
184 
-isPackageLoaded <- function(pkg){
185 
-	stopifnot(is.character(pkg))
186 
-	pkg <- paste("package:", pkg, sep="")
187 
-	pkg %in% search()
171 
+    stopifnot(is.character(cdfName))
172 
+    result <- cdfName %in% validCdfNames()
173 
+    if (!result)
174 
+        warning("cdfName must be one of the following: ",
175 
+                chipList)
176 
+    return(result)
188 177 
 }
189 178
190 179 
 paramNames <- function(){
Browse code

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@50264 bc3139a8-67e5-0310-9ffc-ced21a209358

unknown authored on 16/10/2010 13:23:54
Showing 1 changed files
R/utils.R
History View file @ 34c77ed
... ... 
@@ -168,6 +168,7 @@ validCdfNames <- function(){
168 168 
 	  "human1mduov3b",
169 169 
 	  "humanomni1quadv1b",
170 170 
           "humanomniexpress12v1b",
171 
+	  "humanomni25quadv1b",
171 172 
           "humanimmuno12v1b")
172 173 
 }
173 174 
 isValidCdfName <- function(cdfName){
Browse code

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@49420 bc3139a8-67e5-0310-9ffc-ced21a209358

unknown authored on 16/09/2010 12:01:16
Showing 1 changed files
R/utils.R
History View file @ 0d33470
... ... 
@@ -167,7 +167,8 @@ validCdfNames <- function(){
167 167 
 	  "human660quadv1a",
168 168 
 	  "human1mduov3b",
169 169 
 	  "humanomni1quadv1b",
170 
-          "humanomniexpress12v1b")
170 
+          "humanomniexpress12v1b",
171 
+          "humanimmuno12v1b")
171 172 
 }
172 173 
 isValidCdfName <- function(cdfName){
173 174 
 	chipList <- validCdfNames()
Browse code

Added methods for LinearModelParameter class. removed methods for SnpSuperSet class.

Added a lot of generics for accessing and updating elements in the
LinearModelParameter class.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@48949 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 21/08/2010 02:48:57
Showing 1 changed files
R/utils.R
History View file @ 97e84a8
... ... 
@@ -208,21 +208,7 @@ loadObject <- function(filename, load.it){
208 208 
 	} else return(FALSE)
209 209 
 }
210 210
211 
-initializeParamObject <- function(dimnames){
212 
-	nr <- length(dimnames[[1]])
213 
-	nc <- length(dimnames[[2]])
214 
-	name <- paramNames()
215 
-	ll <- vector("list", length(name))
216 
-	if(isPackageLoaded("ff")){
217 
-		for(i in seq(along=ll)) ll[[i]] <- createFF(name=name[i], dim=c(nr, nc), vmode="double")            ##ff(vmode="double", dim=c(nr, nc), pattern=file.path(ldPath(), name[i]), dimnames=dimnames, overwrite=TRUE)
218 
-		names(ll) <- name
219 
-		ll <- do.call(ffdf, ll)
220 
-	} else {
221 
-		for(i in seq(along=ll)) ll[[i]] <- matrix(NA, nr, nc, dimnames=dimnames)
222 
-		names(ll) <- name
223 
-	}
224 
-	return(ll)
225 
-}
211 
+
226 212
227 213 
 setMethod("annotatedDataFrameFrom", "ff_matrix", Biobase:::annotatedDataFrameFromMatrix)
228 214 
 setMethod("annotatedDataFrameFrom", "ffdf", Biobase:::annotatedDataFrameFromMatrix)
Browse code

Fixed bug in fit.lm functions -- the correlations were assigned incorrectly.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@48923 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 21/08/2010 02:47:23
Showing 1 changed files
R/utils.R
History View file @ 76f72a5
... ... 
@@ -29,11 +29,12 @@ intMedianSummaries <- function(mat, grps)
29 29 
 ## R CMD check
30 30
31 31 
 isLoaded <- function(dataset, environ=.crlmmPkgEnv)
32 
-  exists(dataset, envir=environ)
32 
+	exists(dataset, envir=environ)
33 
+
33 34 
 getVarInEnv <- function(dataset, environ=.crlmmPkgEnv){
34 
-  if (!isLoaded(dataset))
35 
-    stop("Variable ", dataset, " not found in .crlmmPkgEnv")
36 
-  environ[[dataset]]
35 
+	if (!isLoaded(dataset))
36 
+		stop("Variable ", dataset, " not found in .crlmmPkgEnv")
37 
+	environ[[dataset]]
37 38 
 }
38 39
39 40 
 list2SnpSet <- function(x, returnParams=FALSE){
Browse code

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@48480 bc3139a8-67e5-0310-9ffc-ced21a209358

unknown authored on 28/07/2010 02:03:14
Showing 1 changed files
R/utils.R
History View file @ 7d6a129
... ... 
@@ -165,7 +165,8 @@ validCdfNames <- function(){
165 165 
 	  "human610quadv1b",
166 166 
 	  "human660quadv1a",
167 167 
 	  "human1mduov3b",
168 
-	  "humanomni1quadv1b")
168 
+	  "humanomni1quadv1b",
169 
+          "humanomniexpress12v1b")
169 170 
 }
170 171 
 isValidCdfName <- function(cdfName){
171 172 
 	chipList <- validCdfNames()
Browse code

added genotype2 and crlmmCopynumber2

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@45672 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 02/04/2010 03:03:19
Showing 1 changed files
R/utils.R
History View file @ d5bc779
... ... 
@@ -184,23 +184,40 @@ isPackageLoaded <- function(pkg){
184 184 
 }
185 185
186 186 
 paramNames <- function(){
187 
-	c("tau2A", "tau2B", "sig2A", "sig2B",
188 
-	  "nuA", "nuA.se", "nuB",  "nuB.se", "phiA", "phiB", "phiAX", "phiBX",
189 
-	  "phiA.se", "phiB.se", "corr", "corrA.BB", "corrB.AA")
187 
+	c("tau2A",
188 
+	  "tau2B", "sig2A", "sig2B",
189 
+	  "nuA", ##"nuA.se",
190 
+	  "nuB",  ##"nuB.se",
191 
+	  "phiA",
192 
+	  "phiB",
193 
+	  "phiPrimeA",
194 
+	  "phiPrimeB",
195 
+	  ##"phiA.se", "phiB.se",
196 
+	  "corrAB",
197 
+	  "corrBB",
198 
+	  "corrAA")
199 
+}
200 
+
201 
+loadObject <- function(filename, load.it){
202 
+	fname <- paste(filename, ".rda", sep="")
203 
+	if(load.it & file.exists(file.path(ldPath(), fname))){
204 
+		message("load.it is TRUE, loading previously saved ff object")
205 
+		return(TRUE)
206 
+	} else return(FALSE)
190 207 
 }
191 208
192 209 
 initializeParamObject <- function(dimnames){
193 210 
 	nr <- length(dimnames[[1]])
194 
-	nc <- length(dimnames[[2]])
195 
-	ll <- vector("list", 17)
211 
+	nc <- length(dimnames[[2]])
196 212 
 	name <- paramNames()
213 
+	ll <- vector("list", length(name))
197 214 
 	if(isPackageLoaded("ff")){
198 
-		for(i in 1:17) ll[[i]] <- createFF(name=name[i], dim=c(nr, nc), vmode="double")            ##ff(vmode="double", dim=c(nr, nc), pattern=file.path(ldPath(), name[i]), dimnames=dimnames, overwrite=TRUE)
199 
-		names(ll) <- paramNames()
215 
+		for(i in seq(along=ll)) ll[[i]] <- createFF(name=name[i], dim=c(nr, nc), vmode="double")            ##ff(vmode="double", dim=c(nr, nc), pattern=file.path(ldPath(), name[i]), dimnames=dimnames, overwrite=TRUE)
216 
+		names(ll) <- name
200 217 
 		ll <- do.call(ffdf, ll)
201 218 
 	} else {
202 
-		for(i in 1:17) ll[[i]] <- matrix(NA, nr, nc, dimnames=dimnames)
203 
-		names(ll) <- paramNames()
219 
+		for(i in seq(along=ll)) ll[[i]] <- matrix(NA, nr, nc, dimnames=dimnames)
220 
+		names(ll) <- name
204 221 
 	}
205 222 
 	return(ll)
206 223 
 }
Browse code

Fixes in docs and code reorganization

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@45608 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 31/03/2010 11:16:26
Showing 1 changed files
R/utils.R
History View file @ 9ac2da3
... ... 
@@ -205,78 +205,5 @@ initializeParamObject <- function(dimnames){
205 205 
 	return(ll)
206 206 
 }
207 207
208 
-## BC: how about moving initializeBigMatrix to oligoClasses?
209 
-initializeBigMatrix <- function(name, nr, nc, vmode="integer"){
210 
-	if(isPackageLoaded("ff")){
211 
-		if(prod(nr, nc) > 2^31){
212 
-			##Need multiple matrices
213 
-			## -- use ffdf
214 
-			## How many samples per ff object
215 
-			S <- floor(2^31/nr - 1)
216 
-			## How many ff objects
217 
-			L <- ceiling(nc/S)
218 
-			name <- paste(name, 1:L, sep="_")
219 
-			resultsff <- vector("list", L)
220 
-			##resultsB <- vector("list", L)
221 
-			for(i in 1:(L-1)){  ## the Lth object may have fewer than nc columns
222 
-				resultsff[[i]] <- createFF(name=name[i],
223 
-							   dim=c(nr, S),
224 
-							   vmode=vmode)
225 
-			}
226 
-			##the Lth element
227 
-			leftOver <- nc - ((L-1)*S)
228 
-			resultsff[[L]] <- createFF(name=name[L],
229 
-						   dim=c(nr, leftOver),
230 
-						   vmode=vmode)
231 
-			resultsff[[L]][,] <- NA
232 
-			results <- do.call(ffdf, resultsff)
233 
-			rm(resultsff); gc()
234 
-			##dimnames(resultsff) <- dns
235 
-		} else {
236 
-			results <- createFF(name=name,
237 
-					    dim=c(nr, nc),
238 
-					    vmode=vmode)
239 
-			results[,] <- NA
240 
-		}
241 
-	}  else {
242 
-          theNA <- switch(vmode,
243 
-                          integer=NA_integer_,
244 
-                          double=NA_real_,
245 
-                          character=NA_character_,
246 
-                          stop("Mode ", vmode, " not implemented for regular matrices"))
247 
-          results <- matrix(theNA, nr, nc)
248 
-        }
249 
-	return(results)
250 
-}
251 
-
252 
-initializeBigVector <- function(name, n, vmode="integer"){
253 
-  if(isPackageLoaded("ff")){
254 
-    results <- ff(vmode=vmode, length=n, pattern=file.path(ldPath(), basename(name)))
255 
-  }  else {
256 
-    theNA <- switch(vmode,
257 
-                    integer=NA_integer_,
258 
-                    double=NA_real_,
259 
-                    character=NA_character_,
260 
-                    stop("Mode ", vmode, " not implemented for regular matrices"))
261 
-    results <- rep(theNA, n)
262 
-  }
263 
-  return(results)
264 
-}
265 
-
266 
-
267 208 
 setMethod("annotatedDataFrameFrom", "ff_matrix", Biobase:::annotatedDataFrameFromMatrix)
268 209 
 setMethod("annotatedDataFrameFrom", "ffdf", Biobase:::annotatedDataFrameFromMatrix)
269 
-
270 
-
271 
-##annotatedDataFrameFromFF <- function (object, byrow = FALSE, ...){
272 
-##    dims <- dim(object)
273 
-##    if (is.null(dims) || all(dims == 0))
274 
-##        annotatedDataFrameFrom(NULL, byrow = byrow, ...)
275 
-##    else {
276 
-##        N <- if (byrow)  dims[1]       else dims[2]
277 
-##        nms <- if (byrow) rownames(object)  else colnames(object)
278 
-##        data <- data.frame(numeric(N), row.names = nms)[, FALSE]
279 
-##        dimLabels <- if (byrow) c("featureNames", "featureColumns")  else c("sampleNames", "sampleColumns")
280 
-##        new("AnnotatedDataFrame", data = data, dimLabels = dimLabels)
281 
-##    }
282 
-##}
Browse code

HPC for snprma/crlmm on Affy

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@45498 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 25/03/2010 13:14:54
Showing 1 changed files
R/utils.R
History View file @ f0da692
... ... 
@@ -37,7 +37,7 @@ getVarInEnv <- function(dataset, environ=.crlmmPkgEnv){
37 37 
 }
38 38
39 39 
 list2SnpSet <- function(x, returnParams=FALSE){
40 
-  pd <- data.frame(SNR=x[["SNR"]], gender=x[["gender"]],
40 
+  pd <- data.frame(SNR=x[["SNR"]][], gender=x[["gender"]],
41 41 
                    batchQC=rep(x[["batchQC"]], ncol(x[["calls"]])),
42 42 
                    row.names=colnames(x[["calls"]]))
43 43 
   pdv <- data.frame(labelDescription=c("Signal-to-noise Ratio",
... ... 
@@ -205,7 +205,7 @@ initializeParamObject <- function(dimnames){
205 205 
 	return(ll)
206 206 
 }
207 207
208 
-
208 
+## BC: how about moving initializeBigMatrix to oligoClasses?
209 209 
 initializeBigMatrix <- function(name, nr, nc, vmode="integer"){
210 210 
 	if(isPackageLoaded("ff")){
211 211 
 		if(prod(nr, nc) > 2^31){
... ... 
@@ -238,9 +238,32 @@ initializeBigMatrix <- function(name, nr, nc, vmode="integer"){
238 238 
 					    vmode=vmode)
239 239 
 			results[,] <- NA
240 240 
 		}
241 
-	}  else results <- matrix(NA, nr, nc)
241 
+	}  else {
242 
+          theNA <- switch(vmode,
243 
+                          integer=NA_integer_,
244 
+                          double=NA_real_,
245 
+                          character=NA_character_,
246 
+                          stop("Mode ", vmode, " not implemented for regular matrices"))
247 
+          results <- matrix(theNA, nr, nc)
248 
+        }
242 249 
 	return(results)
243 250 
 }
251 
+
252 
+initializeBigVector <- function(name, n, vmode="integer"){
253 
+  if(isPackageLoaded("ff")){
254 
+    results <- ff(vmode=vmode, length=n, pattern=file.path(ldPath(), basename(name)))
255 
+  }  else {
256 
+    theNA <- switch(vmode,
257 
+                    integer=NA_integer_,
258 
+                    double=NA_real_,
259 
+                    character=NA_character_,
260 
+                    stop("Mode ", vmode, " not implemented for regular matrices"))
261 
+    results <- rep(theNA, n)
262 
+  }
263 
+  return(results)
264 
+}
265 
+
266 
+
244 267 
 setMethod("annotatedDataFrameFrom", "ff_matrix", Biobase:::annotatedDataFrameFromMatrix)
245 268 
 setMethod("annotatedDataFrameFrom", "ffdf", Biobase:::annotatedDataFrameFromMatrix)
246 269
Browse code

updates to genotype, crlmmIlluminaRS, and crlmmCopynumber

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@45497 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 25/03/2010 13:01:51
Showing 1 changed files
R/utils.R
History View file @ c00f715
... ... 
@@ -195,7 +195,7 @@ initializeParamObject <- function(dimnames){
195 195 
 	ll <- vector("list", 17)
196 196 
 	name <- paramNames()
197 197 
 	if(isPackageLoaded("ff")){
198 
-		for(i in 1:17) ll[[i]] <- ff(vmode="double", dim=c(nr, nc), pattern=file.path(ldPath(), name[i]), dimnames=dimnames, overwrite=TRUE)
198 
+		for(i in 1:17) ll[[i]] <- createFF(name=name[i], dim=c(nr, nc), vmode="double")            ##ff(vmode="double", dim=c(nr, nc), pattern=file.path(ldPath(), name[i]), dimnames=dimnames, overwrite=TRUE)
199 199 
 		names(ll) <- paramNames()
200 200 
 		ll <- do.call(ffdf, ll)
201 201 
 	} else {
Browse code

updated genotype and crlmmIlluminaRS functions. suppressing integer overflow warnings that do not appear to be relevant

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@45348 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 19/03/2010 16:00:25
Showing 1 changed files
R/utils.R
History View file @ afb508f
... ... 
@@ -236,6 +236,7 @@ initializeBigMatrix <- function(name, nr, nc, vmode="integer"){
236 236 
 			results <- createFF(name=name,
237 237 
 					    dim=c(nr, nc),
238 238 
 					    vmode=vmode)
239 
+			results[,] <- NA
239 240 
 		}
240 241 
 	}  else results <- matrix(NA, nr, nc)
241 242 
 	return(results)
Browse code

update initializeBigMatrix. methods for CNSetLM

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@45324 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 18/03/2010 13:47:33
Showing 1 changed files
R/utils.R
History View file @ fd65333
... ... 
@@ -211,36 +211,34 @@ initializeBigMatrix <- function(name, nr, nc, vmode="integer"){
211 211 
 		if(prod(nr, nc) > 2^31){
212 212 
 			##Need multiple matrices
213 213 
 			## -- use ffdf
214 
-
215 214 
 			## How many samples per ff object
216 215 
 			S <- floor(2^31/nr - 1)
217 
-
218 216 
 			## How many ff objects
219 217 
 			L <- ceiling(nc/S)
220 218 
 			name <- paste(name, 1:L, sep="_")
221 
-
222 
-			results <- vector("list", L)
219 
+			resultsff <- vector("list", L)
223 220 
 			##resultsB <- vector("list", L)
224 221 
 			for(i in 1:(L-1)){  ## the Lth object may have fewer than nc columns
225 
-				results[[i]] <- createFF(name=name[i],
226 
-							 dim=c(nr, S),
227 
-							 vmode=vmode)
222 
+				resultsff[[i]] <- createFF(name=name[i],
223 
+							   dim=c(nr, S),
224 
+							   vmode=vmode)
228 225 
 			}
229 226 
 			##the Lth element
230 227 
 			leftOver <- nc - ((L-1)*S)
231 
-			results[[L]] <- createFF(name=name[L],
232 
-						 dim=c(nr, leftOver),
233 
-						 vmode=vmode)
234 
-			resultsff <- do.call(ffdf, results)
228 
+			resultsff[[L]] <- createFF(name=name[L],
229 
+						   dim=c(nr, leftOver),
230 
+						   vmode=vmode)
231 
+			resultsff[[L]][,] <- NA
232 
+			results <- do.call(ffdf, resultsff)
233 
+			rm(resultsff); gc()
235 234 
 			##dimnames(resultsff) <- dns
236 235 
 		} else {
237 
-			resultsff <- createFF(name=name,
238 
-					      dim=c(nr, nc),
239 
-					      vmode=vmode)
236 
+			results <- createFF(name=name,
237 
+					    dim=c(nr, nc),
238 
+					    vmode=vmode)
240 239 
 		}
241 
-		resultsff[,] <- NA
242 
-	}  else resultsff <- matrix(NA, nr, nc)
243 
-	return(resultsff)
240 
+	}  else results <- matrix(NA, nr, nc)
241 
+	return(results)
244 242 
 }
245 243 
 setMethod("annotatedDataFrameFrom", "ff_matrix", Biobase:::annotatedDataFrameFromMatrix)
246 244 
 setMethod("annotatedDataFrameFrom", "ffdf", Biobase:::annotatedDataFrameFromMatrix)
Browse code

testing crlmmIlluminaRS in cnrma-functions

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@45221 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 15/03/2010 01:43:23
Showing 1 changed files
R/utils.R
History View file @ e1909d6
... ... 
@@ -183,6 +183,29 @@ isPackageLoaded <- function(pkg){
183 183 
 	pkg %in% search()
184 184 
 }
185 185
186 
+paramNames <- function(){
187 
+	c("tau2A", "tau2B", "sig2A", "sig2B",
188 
+	  "nuA", "nuA.se", "nuB",  "nuB.se", "phiA", "phiB", "phiAX", "phiBX",
189 
+	  "phiA.se", "phiB.se", "corr", "corrA.BB", "corrB.AA")
190 
+}
191 
+
192 
+initializeParamObject <- function(dimnames){
193 
+	nr <- length(dimnames[[1]])
194 
+	nc <- length(dimnames[[2]])
195 
+	ll <- vector("list", 17)
196 
+	name <- paramNames()
197 
+	if(isPackageLoaded("ff")){
198 
+		for(i in 1:17) ll[[i]] <- ff(vmode="double", dim=c(nr, nc), pattern=file.path(ldPath(), name[i]), dimnames=dimnames, overwrite=TRUE)
199 
+		names(ll) <- paramNames()
200 
+		ll <- do.call(ffdf, ll)
201 
+	} else {
202 
+		for(i in 1:17) ll[[i]] <- matrix(NA, nr, nc, dimnames=dimnames)
203 
+		names(ll) <- paramNames()
204 
+	}
205 
+	return(ll)
206 
+}
207 
+
208 
+
186 209 
 initializeBigMatrix <- function(name, nr, nc, vmode="integer"){
187 210 
 	if(isPackageLoaded("ff")){
188 211 
 		if(prod(nr, nc) > 2^31){
... ... 
@@ -221,3 +244,17 @@ initializeBigMatrix <- function(name, nr, nc, vmode="integer"){
221 244 
 }
222 245 
 setMethod("annotatedDataFrameFrom", "ff_matrix", Biobase:::annotatedDataFrameFromMatrix)
223 246 
 setMethod("annotatedDataFrameFrom", "ffdf", Biobase:::annotatedDataFrameFromMatrix)
247 
+
248 
+
249 
+##annotatedDataFrameFromFF <- function (object, byrow = FALSE, ...){
250 
+##    dims <- dim(object)
251 
+##    if (is.null(dims) || all(dims == 0))
252 
+##        annotatedDataFrameFrom(NULL, byrow = byrow, ...)
253 
+##    else {
254 
+##        N <- if (byrow)  dims[1]       else dims[2]
255 
+##        nms <- if (byrow) rownames(object)  else colnames(object)
256 
+##        data <- data.frame(numeric(N), row.names = nms)[, FALSE]
257 
+##        dimLabels <- if (byrow) c("featureNames", "featureColumns")  else c("sampleNames", "sampleColumns")
258 
+##        new("AnnotatedDataFrame", data = data, dimLabels = dimLabels)
259 
+##    }
260 
+##}
Browse code

added genotype function to cnrma-functions. Added AllClasses.R file to set ff_matrix and ffdf classes

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@45165 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 11/03/2010 11:02:23
Showing 1 changed files
R/utils.R
History View file @ e272e5d
... ... 
@@ -155,7 +155,69 @@ celDates <- function(celfiles){
155 155 
 	return(celdts)
156 156 
 }
157 157
158 
+validCdfNames <- function(){
159 
+	c("genomewidesnp6",
160 
+	  "genomewidesnp5",
161 
+	  "human370v1c",
162 
+	  "human370quadv3c",
163 
+	  "human550v3b",
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+	  "human650v3a",
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+	  "human610quadv1b",
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+	  "human660quadv1a",
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+	  "human1mduov3b",
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+	  "humanomni1quadv1b")
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+}
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+isValidCdfName <- function(cdfName){
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+	chipList <- validCdfNames()
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+	result <- cdfName %in% chipList
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+	if(!(result)){
174 
+		warning("cdfName must be one of the following: ",
175 
+			chipList)
176 
+	}
177 
+	return(result)
178 
+}
158 179
180 
+isPackageLoaded <- function(pkg){
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+	stopifnot(is.character(pkg))
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+	pkg <- paste("package:", pkg, sep="")
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+	pkg %in% search()
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+}
159 185
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+initializeBigMatrix <- function(name, nr, nc, vmode="integer"){
187 
+	if(isPackageLoaded("ff")){
188 
+		if(prod(nr, nc) > 2^31){
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+			##Need multiple matrices
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+			## -- use ffdf
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+
192 
+			## How many samples per ff object
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+			S <- floor(2^31/nr - 1)
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+
195 
+			## How many ff objects
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+			L <- ceiling(nc/S)
197 
+			name <- paste(name, 1:L, sep="_")
198 
+
199 
+			results <- vector("list", L)
200 
+			##resultsB <- vector("list", L)
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+			for(i in 1:(L-1)){  ## the Lth object may have fewer than nc columns
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+				results[[i]] <- createFF(name=name[i],
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+							 dim=c(nr, S),
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+							 vmode=vmode)
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+			}
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+			##the Lth element
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+			leftOver <- nc - ((L-1)*S)
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+			results[[L]] <- createFF(name=name[L],
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+						 dim=c(nr, leftOver),
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+						 vmode=vmode)
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+			resultsff <- do.call(ffdf, results)
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+			##dimnames(resultsff) <- dns
213 
+		} else {
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+			resultsff <- createFF(name=name,
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+					      dim=c(nr, nc),
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+					      vmode=vmode)
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+		}
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+		resultsff[,] <- NA
219 
+	}  else resultsff <- matrix(NA, nr, nc)
220 
+	return(resultsff)
221 
+}
160 222 
 setMethod("annotatedDataFrameFrom", "ff_matrix", Biobase:::annotatedDataFrameFromMatrix)
161 223 
 setMethod("annotatedDataFrameFrom", "ffdf", Biobase:::annotatedDataFrameFromMatrix)
Browse code

added annotatedDataFrameFrom methods for ff_matrix and ffdf

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@45129 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 10/03/2010 11:45:52
Showing 1 changed files
R/utils.R
History View file @ a4ece85
... ... 
@@ -157,4 +157,5 @@ celDates <- function(celfiles){
157 157
158 158
159 159
160 
-
160 
+setMethod("annotatedDataFrameFrom", "ff_matrix", Biobase:::annotatedDataFrameFromMatrix)
161 
+setMethod("annotatedDataFrameFrom", "ffdf", Biobase:::annotatedDataFrameFromMatrix)
Browse code

roll back to crlmm version 1.5.24

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@45126 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 10/03/2010 01:27:04
Showing 1 changed files
R/utils.R
History View file @ 5fcfed7
... ... 
@@ -155,235 +155,6 @@ celDates <- function(celfiles){
155 155 
 	return(celdts)
156 156 
 }
157 157
158 
-isPackageLoaded <- function(pkg){
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-	stopifnot(is.character(pkg))
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-	pkg <- paste("package:", pkg, sep="")
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-	pkg %in% search()
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-}
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-
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-validCdfNames <- function(){
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-	c("genomewidesnp6",
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-	  "genomewidesnp5",
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-	  "human370v1c",
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-	  "human370quadv3c",
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-	  "human550v3b",
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-	  "human650v3a",
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-	  "human610quadv1b",
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-	  "human660quadv1a",
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-	  "human1mduov3b",
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-	  "humanomni1quadv1b")
175 
-}
176 
-
177 
-isValidCdfName <- function(cdfName){
178 
-	chipList <- validCdfNames()
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-	result <- cdfName %in% chipList
180 
-	if(!(result)){
181 
-		warning("cdfName must be one of the following: ",
182 
-			chipList)
183 
-	}
184 
-	return(result)
185 
-}
186 
-
187 
-initializeBigMatrix <- function(dns, vmode="integer"){
188 
-##initializeBigMatrix <- function(nr, nc, vmode="integer"){
189 
-	nr <- length(dns[[1]])
190 
-	nc <- length(dns[[2]])
191 
-	if(isPackageLoaded("ff")){
192 
-	if(prod(nr, nc) > 2^31){
193 
-		##Need multiple matrices
194 
-		## -- use ffdf
195 
-
196 
-		## How many samples per ff object
197 
-		S <- floor(2^31/nr - 1)
198 
-
199 
-		## How many ff objects
200 
-		L <- ceiling(nc/S)
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-
202 
-		results <- vector("list", L)
203 
-		##resultsB <- vector("list", L)
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-		for(i in 1:(L-1)){  ## the Lth object may have fewer than nc columns
205 
-			results[[i]] <- ff(dim=c(nr, S),
206 
-					   vmode=vmode,
207 
-					   finalizer="close",
208 
-					   overwrite=TRUE)
209 
-		}
210 
-		##the Lth element
211 
-		leftOver <- nc - ((L-1)*S)
212 
-		results[[L]] <- ff(dim=c(nr, leftOver),
213 
-				   vmode=vmode,
214 
-				   finalizer="close",
215 
-				   overwrite=TRUE)
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-		resultsff <- do.call(ffdf, results)
217 
-		##dimnames(resultsff) <- dns
218 
-	} else {
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-		resultsff <- ff(dim=c(nr, nc),
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-				vmode=vmode,
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-				finalizer="close",
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-				overwrite=TRUE)
223 
-##				dimnames=dns)
224 
-	}
225 
-	resultsff[,] <- NA
226 
-}  else resultsff <- matrix(NA, nr, nc)
227 
-	return(resultsff)
228 
-}
229 
-
230 
-paramNames <- function(){
231 
-	c("tau2A", "tau2B", "sig2A", "sig2B",
232 
-	  "nuA", "nuB", "nuA.se", "nuB.se", "phiA", "phiB", "phiA2", "phiB2",
233 
-	  "phiA.se", "phiB.se", "corr", "corrA.BB", "corrB.AA")
234 
-}
235 158
236 
-initializeParamObject <- function(dimnames){
237 
-	nr <- length(dimnames[[1]])
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-	nc <- length(dimnames[[2]])
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-	ll <- vector("list", 17)
240 
-	if(isPackageLoaded("ff")){
241 
-		for(i in 1:17) ll[[i]] <- ff(dim=c(nr,nc), vmode="double", finalizer="close", dimnames=dimnames, overwrite=TRUE)
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-		names(ll) <- paramNames()
243 
-		ll <- do.call(ffdf, ll)
244 
-	} else {
245 
-		for(i in 1:17) ll[[i]] <- matrix(NA, nr, nc, dimnames=dimnames)
246 
-		names(ll) <- paramNames()
247 
-	}
248 
-	return(ll)
249 
-}
250 159
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-whichPlatform <- function(cdfName){
252 
-	index <- grep("genomewidesnp", cdfName)
253 
-	if(length(index) > 0){
254 
-		platform <- "Affymetrix"
255 
-	} else{
256 
-		index <- grep("human", cdfName)
257 
-		platform <- "Illumina"
258 
-	}
259 
-	return(platform)
260 
-}
261 
-
262 
-updateParams <- function(cnParams, object, row.index, batch){
263 
-	labels.asis <- fvarLabels(object)[4:20]
264 
-	B <- batch
265 
-	batch <- paste("_", batch, sep="")
266 
-	labels <- as.character(sapply(labels.asis, function(x, batch) strsplit(x, batch)[[1]][1], batch=batch))
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-	labels <- gsub("X", "2", labels)
268 
-	if(!isPackageLoaded("ff")){
269 
-		##batch <- paste("_", strsplit(labels.asis[1], batch), sep="")
270 
-		##labels <- gsub("_", "\\.", labels.asis)
271 
-		##labels <- gsub(paste("\\.", batch, sep=""), "", labels)
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-		j <- match(B, colnames(cnParams[[1]]))
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-		for(i in seq(along=labels)){
274 
-			ii <- match(labels[i], names(cnParams))
275 
-			jj <- match(labels.asis[i], fvarLabels(object))
276 
-			cnParams[[ii]][, j] <- fData(object)[, jj]
277 
-		}
278 
-	} else {
279 
-		##labels <- as.character(sapply(labels.asis, function(x, batch) strsplit(x, batch)[[1]][1], batch=batch))
280 
-		##labels <- gsub("_", "\\.", labels.asis)
281 
-		##labels <- gsub("X", "2", labels)
282 
-		col.index <- match(labels, colnames(cnParams))
283 
-		cnParams[row.index, col.index] <- fData(object)[, 4:20]
284 
-	}
285 
-	return(cnParams)
286 
-}
287 160
288 
-##			tau2A[row.index, i] <- getParam(cnSet, "tau2A", unique(batch)[i])
289 
-##			tau2B[row.index, i] <- getParam(cnSet, "tau2B", unique(batch)[i])
290 
-##			sig2A[row.index, i] <- getParam(cnSet, "sig2A", unique(batch)[i])
291 
-##			sig2B[row.index, i] <- getParam(cnSet, "sig2B", unique(batch)[i])
292 
-##			nuA[row.index, i] <- getParam(cnSet, "nuA", unique(batch)[i])
293 
-##			nuA.se[row.index, i] <- getParam(cnSet, "nuA.se", unique(batch)[i])
294 
-##			nuB[row.index, i] <- getParam(cnSet, "nuB", unique(batch)[i])
295 
-##			nuB.se[row.index, i] <- getParam(cnSet, "nuB.se", unique(batch)[i])
296 
-##			phiA[row.index, i] <- getParam(cnSet, "phiA", unique(batch)[i])
297 
-##			phiA.se[row.index, i] <- getParam(cnSet, "phiA.se", unique(batch)[i])
298 
-##			phiB[row.index, i] <- getParam(cnSet, "phiB", unique(batch)[i])
299 
-##			phiB.se[row.index, i] <- getParam(cnSet, "phiB.se", unique(batch)[i])
300 
-##			corr[row.index, i] <- getParam(cnSet, "corr", unique(batch)[i])
301 
-##			corrA.BB[row.index, i] <- getParam(cnSet, "corrA.BB", unique(batch)[i])
302