* collab_release:
Edits to getAvailableIlluminaGenomeBuild and getFeatureData for compatibility with annotation packages from the 2.10 release cycle
m the 2.10 release cycle
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git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_11/madman/Rpacks/crlmm@70731 bc3139a8-67e5-0310-9ffc-ced21a209358
Rob Scharp authored on 23/10/2012 13:58:56 | ... | ... |
@@ -1,7 +1,7 @@ |
| 1 | 1 |
Package: crlmm |
| 2 | 2 |
Type: Package |
| 3 | 3 |
Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays. |
| 4 |
-Version: 1.16.1 |
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| 4 |
+Version: 1.16.2 |
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| 5 | 5 |
Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo Ruczinski, Rafael A Irizarry |
| 6 | 6 |
Maintainer: Benilton S Carvalho <Benilton.Carvalho@cancer.org.uk>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.EDU.AU> |
| 7 | 7 |
Description: Faster implementation of CRLMM specific to SNP 5.0 and 6.0 arrays, as well as a copy number tool specific to 5.0, 6.0, and Illumina platforms |
| ... | ... |
@@ -41,15 +41,31 @@ getFeatureData <- function(cdfName, copynumber=FALSE, genome){
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| 41 | 41 |
} |
| 42 | 42 |
path <- system.file("extdata", package=pkgname)
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| 43 | 43 |
##multiple.builds <- length(grep("hg19", list.files(path)) > 0)
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| 44 |
- if(missing(genome)){
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- snp.file <- list.files(path, pattern="snpProbes_hg") |
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| 46 |
- if(length(snp.file) > 1){
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- ## use hg19 |
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- message("genome build not specified. Using build hg19 for annotation.")
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- snp.file <- snp.file[1] |
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- } |
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- genome <- gsub(".rda", "", strsplit(snp.file, "snpProbes_")[[1]][[2]])
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- } else snp.file <- paste("snpProbes_", genome, ".rda", sep="")
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+## if(missing(genome)){
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+## snp.file <- list.files(path, pattern="snpProbes_hg") |
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+## if(length(snp.file) > 1){
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+## ## use hg19 |
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+## message("genome build not specified. Using build hg19 for annotation.")
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+## snp.file <- snp.file[1] |
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+## } |
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+## genome <- gsub(".rda", "", strsplit(snp.file, "snpProbes_")[[1]][[2]])
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+## } else snp.file <- paste("snpProbes_", genome, ".rda", sep="")
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+ snp.file <- list.files(path, pattern="snpProbes_hg") |
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+ if(length(snp.file)==0){
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+ no.build <- TRUE |
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+ snp.file <- list.files(path, pattern="snpProbes.rda") |
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+ } else {
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+ no.build <- FALSE |
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+ if(missing(genome)){
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+ snp.file <- list.files(path, pattern="snpProbes_hg") |
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+ if(length(snp.file) > 1){
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+ ## use hg19 |
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+ message("genome build not specified. Using build hg19 for annotation.")
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+ snp.file <- snp.file[1] |
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+ } |
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+ genome <- gsub(".rda", "", strsplit(snp.file, "snpProbes_")[[1]][[2]])
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+ } else snp.file <- paste("snpProbes_", genome, ".rda", sep="")
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+ } |
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| 53 | 69 |
## if(!multiple.builds){
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| 54 | 70 |
## load(file.path(path, "snpProbes.rda")) |
| 55 | 71 |
## } else load(file.path(path, paste("snpProbes_", genome, ".rda", sep="")))
|
| ... | ... |
@@ -58,7 +74,10 @@ getFeatureData <- function(cdfName, copynumber=FALSE, genome){
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| 58 | 74 |
## if we use a different build we may throw out a number of snps... |
| 59 | 75 |
snpProbes <- snpProbes[rownames(snpProbes) %in% gns, ] |
| 60 | 76 |
if(copynumber){
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- cn.file <- paste("cnProbes_", genome, ".rda", sep="")
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+## cn.file <- paste("cnProbes_", genome, ".rda", sep="")
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+ if(!no.build){
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+ cn.file <- paste("cnProbes_", genome, ".rda", sep="")
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+ } else cn.file <- "cnProbes.rda" |
|
| 62 | 81 |
load(file.path(path, cn.file)) |
| 63 | 82 |
## if(!multiple.builds){
|
| 64 | 83 |
## load(file.path(path, "cnProbes.rda")) |
| ... | ... |
@@ -1072,6 +1072,16 @@ getProtocolData.Illumina = function(filenames, sep="_", fileExt="Grn.idat", verb |
| 1072 | 1072 |
return(protocoldata) |
| 1073 | 1073 |
} |
| 1074 | 1074 |
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+##getAvailableIlluminaGenomeBuild <- function(path){
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+## snp.file <- list.files(path, pattern="snpProbes_hg") |
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+## if(length(snp.file) > 1){
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+## ## use hg19 |
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+## message("genome build not specified. Using build hg19 for annotation.")
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+## snp.file <- snp.file[1] |
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+## } |
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+## genome <- gsub(".rda", "", strsplit(snp.file, "snpProbes_")[[1]][[2]])
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+##} |
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+ |
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| 1075 | 1085 |
getAvailableIlluminaGenomeBuild <- function(path){
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| 1076 | 1086 |
snp.file <- list.files(path, pattern="snpProbes_hg") |
| 1077 | 1087 |
if(length(snp.file) > 1){
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| ... | ... |
@@ -1079,7 +1089,10 @@ getAvailableIlluminaGenomeBuild <- function(path){
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| 1079 | 1089 |
message("genome build not specified. Using build hg19 for annotation.")
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| 1080 | 1090 |
snp.file <- snp.file[1] |
| 1081 | 1091 |
} |
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- genome <- gsub(".rda", "", strsplit(snp.file, "snpProbes_")[[1]][[2]])
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+ if(length(snp.file) == 1) |
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+ genome <- gsub(".rda", "", strsplit(snp.file, "snpProbes_")[[1]][[2]])
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+ if(length(snp.file)==0) genome <- "" |
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+ genome |
|
| 1083 | 1096 |
} |
| 1084 | 1097 |
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| 1085 | 1098 |
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