Browse code

Removed crlmm::: from .R files and set saveDate=FALSE in genotype.Illumina() man page to clean up Notes and Warnings

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@88085 bc3139a8-67e5-0310-9ffc-ced21a209358

unknown authored on 28/03/2014 12:43:01
Showing4 changed files

... ...
@@ -2,8 +2,8 @@ Package: crlmm
2 2
 Type: Package
3 3
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for
4 4
         Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
5
-Version: 1.21.7
6
-Date: Mon Mar 10 10:06:36 EST 2014
5
+Version: 1.21.8
6
+Date: Fri Mar 28 16:26:10 EST 2014
7 7
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo
8 8
         Ruczinski, Rafael A Irizarry
9 9
 Maintainer: Benilton S Carvalho <Benilton.Carvalho@cancer.org.uk>,
... ...
@@ -21,7 +21,7 @@ Imports: methods, Biobase (>= 2.15.4), BiocGenerics, affyio (>=
21 21
         utils, lattice, ff, foreach, RcppEigen (>= 0.3.1.2.1),
22 22
         matrixStats, VGAM
23 23
 Suggests: hapmapsnp6, genomewidesnp6Crlmm (>= 1.0.7), GGdata, snpStats,
24
-        ellipse, RUnit, VGAM
24
+        RUnit
25 25
 Collate: AllGenerics.R AllClasses.R methods-AssayData.R methods-CNSet.R
26 26
         methods-CNSetLM.R methods-eSet.R methods-SnpSuperSet.R
27 27
         methods-PredictionRegion.R cnrma-functions.R cnset-accessors.R
... ...
@@ -1127,7 +1127,7 @@ preprocessInf <- function(cnSet,
1127 1127
 	sampleBatches <- splitIndicesByLength(seq_len(ncol(cnSet)), ocSamples()/getDoParWorkers())
1128 1128
 	mixtureParams = initializeBigMatrix("crlmmMixt-", 4, narrays, "double")
1129 1129
 	ocLapply(seq_along(sampleBatches),
1130
-		 crlmm:::processIDAT,
1130
+		 processIDAT, # crlmm:::
1131 1131
 		 sampleBatches=sampleBatches,
1132 1132
 		 sampleSheet=sampleSheet,
1133 1133
 		 arrayNames=arrayNames,
... ...
@@ -571,7 +571,7 @@ calculateRBafCNSet <- function(object, batch.name, chrom){
571 571
 		for(j in seq_along(sampleindex)){
572 572
 			bname <- batch.name[j]
573 573
 			J <- sampleindex[[j]]
574
-			res <- crlmm:::calculateRTheta(object=object,
574
+			res <- calculateRTheta(object=object, # crlmm:::
575 575
 						       batch.name=bname,
576 576
 						       feature.index=i)
577 577
 			k <- match(sampleNames(object)[J], sns)
... ...
@@ -11,7 +11,7 @@
11 11
 genotype.Illumina(sampleSheet=NULL, arrayNames=NULL, ids=NULL, path=".",
12 12
       arrayInfoColNames=list(barcode="SentrixBarcode_A", position="SentrixPosition_A"),
13 13
       highDensity=FALSE, sep="_", fileExt=list(green="Grn.idat", red="Red.idat"), XY=NULL,
14
-      call.method="crlmm", trueCalls=NULL, cdfName, copynumber=TRUE, batch=NULL, saveDate=TRUE, stripNorm=TRUE, 
14
+      call.method="crlmm", trueCalls=NULL, cdfName, copynumber=TRUE, batch=NULL, saveDate=FALSE, stripNorm=TRUE, 
15 15
       useTarget=TRUE, quantile.method="between", mixtureSampleSize=10^5, fitMixture=TRUE,                               
16 16
       eps =0.1, verbose = TRUE, seed = 1, sns, probs = rep(1/3, 3), DF = 6, SNRMin = 5, 
17 17
       recallMin = 10, recallRegMin = 1000, gender = NULL, returnParams = TRUE, badSNP = 0.7)