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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
Showing4 changed files

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@@ -2,8 +2,8 @@ Package: crlmm
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 Type: Package
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 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for
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         Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
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-Version: 1.23.3
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-Date: Fri Sep 19 10:10:31 EDT 2014
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+Version: 1.23.4
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+Date: Thu Sep 25 21:06:19 EST 2014
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 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo
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         Ruczinski, Rafael A Irizarry
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 Maintainer: Benilton S Carvalho <Benilton.Carvalho@cancer.org.uk>,
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@@ -330,6 +330,7 @@ RGtoXY = function(RG, chipType, verbose=TRUE) {
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 	  "humanomniexpress12v1b",  # Omni express 12
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 	  "humanimmuno12v1b",       # Immuno chip 12
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           "humancytosnp12v2p1h",    # CytoSNP 12
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+          "humanexome12v1p2a",      # Exome 12 v1.2 A
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           "humanomniexpexome8v1p1b") # Omni Express Exome 8 v1.1b
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 	  ## RS: added cleancdfname()
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 	  if(missing(chipType)){
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@@ -1258,7 +1259,8 @@ genotype.Illumina <- function(sampleSheet=NULL,
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 	                    "humanomni25quadv1b",     # Omni2.5 quad
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 	                    "humanomni258v1a",        # Omni2.5 8 v1 A
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                             "humanomni258v1p1b",      # Omni2.5 8 v1.1 B
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-                            "humanomni5quadv1b")      # Omni5 quad
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+                            "humanomni5quadv1b",      # Omni5 quad
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+			    "humanexome12v1p2a")      # Exome 12 v1.2 A
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         crlmm.supported = c("human1mv1c",             # 1M
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                             "human370v1c",            # 370CNV
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 	                    "human650v3a",            # 650Y
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@@ -159,6 +159,10 @@ calculatePriorValues <- function(M, numSNP, verbose) {
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     stopCluster(cl) 
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     centers <- matrix(centers, numSNP, 3, byrow = TRUE)
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     priormeans = apply(centers, 2, FUN="median", na.rm=TRUE)
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+       if(abs(sum(priormeans))>1)
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+        checksymmetric= apply(centers,1,function(x){abs(sum(x))})<1
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+      priormeans=apply(centers[checksymmetric,],2, FUN="median", na.rm=TRUE)
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+ 
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     if (verbose) message("Done calculating Prior Means")
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     return(priormeans)
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 }
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@@ -172,6 +172,7 @@ illuminaCdfNames <- function(){
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 	  "humanomniexpress12v1b",  # Omni express 12
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 	  "humanimmuno12v1b",       # Immuno chip 12
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 	  "humancytosnp12v2p1h",    # CytoSNP 12
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+          "humanexome12v1p2a",      # Exome 12 v1.2 A
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           "humanomniexpexome8v1p1b")
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 }
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