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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
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@@ -548,3 +548,7 @@ function (which expects ff objects and supports parallel processing)
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 ** Exported crlmmIlluminaV2(), which combines reading in of idats and genotyping in one.  Also added a man page for this function
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 ** Added close() statements to readIdatFiles(), RGtoXY() and stripNormalize().  Added open() statement to stripNormalize(). Moved close() statement in preprocessInfinium2()
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 ** tidied up crlmm-illumina.R, removing commented out code.
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+
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+2010-09-16 M. Ritchie 1.7.13
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+** added immuno chip 12 as one of the chip options for Illumina.
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+
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@@ -1,8 +1,8 @@
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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: 1.7.13
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-Date: 2010-08-30
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+Version: 1.7.14
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+Date: 2010-09-16
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 Author: Benilton S Carvalho <carvalho@bclab.org>, 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 <carvalho@bclab.org>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.EDU.AU>
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 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
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@@ -40,4 +40,3 @@ Collate: AllGenerics.R
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          zzz.R
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 LazyLoad: yes
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 biocViews: Microarray, Preprocessing, SNP, Bioinformatics, CopyNumberVariants
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-
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@@ -419,7 +419,8 @@ RGtoXY = function(RG, chipType, verbose=TRUE) {
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                "human550v3b",            # 550K
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                "human1mduov3b",          # 1M Duo
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                "humanomni1quadv1b",      # Omni1 quad
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-	       "humanomniexpress12v1b")  # Omni express 12
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+	       "humanomniexpress12v1b",  # Omni express 12
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+               "humanimmuno12v1b")       # Immuno chip 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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@@ -167,7 +167,8 @@ validCdfNames <- function(){
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 	  "human660quadv1a",
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 	  "human1mduov3b",
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 	  "humanomni1quadv1b",
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-          "humanomniexpress12v1b")
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+          "humanomniexpress12v1b",
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+          "humanimmuno12v1b")
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 }
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 isValidCdfName <- function(cdfName){
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 	chipList <- validCdfNames()