removed trace call in illumina copynumber vignette
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_6/madman/Rpacks/crlmm@48447 bc3139a8-67e5-0310-9ffc-ced21a209358
Rob Scharp authored on 27/07/2010 03:01:41
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@@ -55,8 +55,8 @@ importFrom(ellipse, ellipse) |
| 55 | 55 |
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| 56 | 56 |
importFrom(ff, ffdf) |
| 57 | 57 |
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| 58 |
-exportClasses(CNSetLM, list_or_ffdf, ffdf) |
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| 59 |
-exportMethods(open, "[", show, lM, copyNumber, totalCopyNumber) |
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+exportClasses(CNSetLM, ffdf, list) |
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+exportMethods(open, "[", show, lM, copyNumber) ##, totalCopyNumber) |
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| 60 | 60 |
export(crlmm, |
| 61 | 61 |
crlmmCopynumber, |
| 62 | 62 |
crlmmIllumina, |
| ... | ... |
@@ -236,7 +236,7 @@ readIdatFiles2 <- function(sampleSheet=NULL, |
| 236 | 236 |
stop("Cannot find .idat files")
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| 237 | 237 |
if(length(grnfiles)!=length(redfiles)) |
| 238 | 238 |
stop("Cannot find matching .idat files")
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| 239 |
- if(path[1] != "."){
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+ if(path[1] != "." & path[1] != ""){
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| 240 | 240 |
grnidats = file.path(path, grnfiles) |
| 241 | 241 |
redidats = file.path(path, redfiles) |
| 242 | 242 |
} else {
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| ... | ... |
@@ -114,34 +114,6 @@ setMethod("copyNumber", "CNSet", function(object){
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| 114 | 114 |
CN |
| 115 | 115 |
}) |
| 116 | 116 |
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-setMethod("totalCopyNumber", "CNSet", function(object, i, j){
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| 118 |
- if(missing(i) & missing(j)){
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- if(inherits(CA(object), "ff") | inherits(CA(object), "ffdf")) stop("Must specify i and/or j for ff objects")
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- } |
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- if(missing(i) & !missing(j)){
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- snp.index <- which(isSnp(object)) |
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- cn.total <- as.matrix(CA(cnSet)[, j]) |
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- cb <- as.matrix(CB(cnSet)[snp.index, j] ) |
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- cn.total[snp.index, ] <- cn.total[snp.index, ] + cb |
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- } |
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- if(!missing(i) & missing(j)){
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- snp.index <- intersect(which(isSnp(object)), i) |
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- cn.total <- as.matrix(CA(cnSet)[i, ]) |
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- cb <- as.matrix(CB(cnSet)[snp.index, ]) |
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- cn.total[snp.index, ] <- cn.total[snp.index, ] + cb |
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- } |
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- if(!missing(i) & !missing(j)){
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- snp.index <- intersect(which(isSnp(object)), i) |
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- cn.total <- as.matrix(CA(cnSet)[i, j]) |
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- cb <- as.matrix(CB(cnSet)[snp.index, j]) |
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- cn.total[snp.index, ] <- cn.total[snp.index, ] + cb |
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- } |
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- cn.total <- cn.total/100 |
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- dimnames(cn.total) <- NULL |
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- return(cn.total) |
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| 142 |
-}) |
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| 143 |
- |
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- |
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| 145 | 117 |
setMethod("ellipse", "CNSet", function(x, copynumber, batch, ...){
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| 146 | 118 |
ellipse.CNSet(x, copynumber, batch, ...) |
| 147 | 119 |
}) |
| ... | ... |
@@ -299,7 +299,7 @@ The following helper function can facilitate access to the total copy |
| 299 | 299 |
number. |
| 300 | 300 |
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| 301 | 301 |
<<copyNumberHelper>>= |
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-trace(totalCopyNumber, browser, signature="CNSet") |
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| 302 |
+##trace(totalCopyNumber, browser, signature="CNSet") |
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| 303 | 303 |
cn.total2 <- totalCopyNumber(cnSet, i=which(chromosome(cnSet)==1), j=1:20) |
| 304 | 304 |
@ |
| 305 | 305 |
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