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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
Showing5 changed files

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@@ -1,7 +1,7 @@
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 Package: crlmm
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 Type: Package
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 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
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-Version: 1.11.3
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+Version: 1.11.4
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 Date: 2010-12-10
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 Author: Benilton S Carvalho <Benilton.Carvalho@cancer.org.uk>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.edu.au>, Ingo Ruczinski <iruczins@jhsph.edu>, Rafael A Irizarry
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 Maintainer: Benilton S Carvalho <Benilton.Carvalho@cancer.org.uk>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.EDU.AU>
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@@ -413,7 +413,7 @@ RGtoXY = function(RG, chipType, verbose=TRUE) {
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   needToLoad <- !all(sapply(c('addressA', 'addressB', 'base'), isLoaded))
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   if(needToLoad){
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-	  chipList = c("human1mv1c",             # 1M
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+	  chipList = c("human1mv1c",# 1M
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 	  "human370v1c",            # 370CNV
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 	  "human650v3a",            # 650Y
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 	  "human610quadv1b",        # 610 quad
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@@ -424,7 +424,8 @@ RGtoXY = function(RG, chipType, verbose=TRUE) {
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 	  "humanomni1quadv1b",      # Omni1 quad
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 	  "humanomni25quadv1b",     # Omni2.5 quad
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 	  "humanomniexpress12v1b",  # Omni express 12
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-	  "humanimmuno12v1b")       # Immuno chip 12
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+	  "humanimmuno12v1b",       # Immuno chip 12
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+          "humancytosnp12v2p1h")    # CytoSNP 12
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 	  if(missing(chipType)){
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 		  chipType = match.arg(annotation(RG), chipList)
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 	  } else chipType = match.arg(chipType, chipList)
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@@ -165,7 +165,8 @@ validCdfNames <- function(){
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 	  "humanomni1quadv1b",
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           "humanomniexpress12v1b",
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 	  "humanomni25quadv1b",
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-          "humanimmuno12v1b")
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+          "humanimmuno12v1b",
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+          "humancytosnp12v2p1h")
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 }
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 isValidCdfName <- function(cdfName){
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 	chipList <- validCdfNames()
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@@ -38,7 +38,7 @@ crlmmIllumina(RG, XY, stripNorm=TRUE,
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   \item{cdfName}{'character' defining the chip annotation (manifest) to use
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     ('human370v1c', human550v3b', 'human650v3a', 'human1mv1c',
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     'human370quadv3c', 'human610quadv1b', 'human660quadv1a',
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-    'human1mduov3b', 'humanomni1quadv1b', 'humanomniexpress12v1b')}
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+    'human1mduov3b', 'humanomni1quadv1b', 'humanomniexpress12v1b', 'humancytosnp12v2p1h')}
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   \item{sns}{'character' vector with sample names to be used.}
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   \item{recallMin}{'integer'. Minimum number of samples for recalibration.}
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   \item{recallRegMin}{'integer'. Minimum number of SNP's for regression.}
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@@ -64,7 +64,7 @@ crlmmIlluminaV2(sampleSheet=NULL, arrayNames=NULL, ids=NULL, path=".",
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   \item{cdfName}{'character' defining the chip annotation (manifest) to use
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     ('human370v1c', human550v3b', 'human650v3a', 'human1mv1c',
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     'human370quadv3c', 'human610quadv1b', 'human660quadv1a',
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-    'human1mduov3b', 'humanomni1quadv1b', 'humanomniexpress12v1b')}
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+    'human1mduov3b', 'humanomni1quadv1b', 'humanomniexpress12v1b', 'humancytosnp12v2p1h')}
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   \item{sns}{'character' vector with sample names to be used.}
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   \item{recallMin}{'integer'. Minimum number of samples for recalibration.}
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   \item{recallRegMin}{'integer'. Minimum number of SNP's for regression.}