Added testing.Rnw and testingFF.Rnw to Makefile
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@48960 bc3139a8-67e5-0310-9ffc-ced21a209358
... | ... |
@@ -51,13 +51,15 @@ getFeatureData.Affy <- function(cdfName, copynumber=FALSE){ |
51 | 51 |
return(new("AnnotatedDataFrame", data=data.frame(M))) |
52 | 52 |
} |
53 | 53 |
|
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-construct <- function(filenames, cdfName, copynumber=FALSE, |
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+construct <- function(filenames, |
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+ cdfName, |
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+ copynumber=TRUE, |
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55 | 57 |
sns, verbose=TRUE, batch, fns){ |
56 | 58 |
if(!missing(batch)){ |
57 | 59 |
stopifnot(length(batch) == length(sns)) |
58 | 60 |
} |
59 | 61 |
if(missing(sns) & missing(filenames)) stop("one of filenames or samplenames (sns) must be provided") |
60 |
- if(verbose) message("Initializing container for assay data elements alleleA, alleleB, call, callProbability") |
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+ if(verbose) message("Initializing container for copy number estimation") |
|
61 | 63 |
featureData <- getFeatureData.Affy(cdfName, copynumber=copynumber) |
62 | 64 |
if(!missing(fns)){ |
63 | 65 |
index <- match(fns, featureNames(featureData)) |
... | ... |
@@ -254,9 +256,8 @@ genotype <- function(filenames, |
254 | 256 |
A(callSet)[snp.index, ] <- snprmaRes[["A"]] |
255 | 257 |
B(callSet)[snp.index, ] <- snprmaRes[["B"]] |
256 | 258 |
} |
257 |
-## stopifnot(identical(featureNames(callSet)[snp.index], snprmaRes$gns)) |
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- pData(callSet)$SKW <- snprmaRes$SKW |
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- pData(callSet)$SNR <- snprmaRes$SNR |
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+ pData(callSet)$SKW <- snprmaRes[["SKW"]] |
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+ pData(callSet)$SNR <- snprmaRes[["SNR"]] |
|
260 | 261 |
mixtureParams <- snprmaRes$mixtureParams |
261 | 262 |
np.index <- which(!is.snp) |
262 | 263 |
if(verbose) message("Normalizing nonpolymorphic markers") |
... | ... |
@@ -432,7 +432,7 @@ setReplaceMethod("snpCall", c("CNSet", "ff_or_matrix"), |
432 | 432 |
function(object, ..., value){ |
433 | 433 |
assayDataElementReplace(object, "call", value) |
434 | 434 |
}) |
435 |
-setReplaceMethod("snpCallProbability", c("CNSet", "ff_or_matrix"), |
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- function(object, ..., value){ |
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- assayDataElementReplace(object, "callProbability", value) |
|
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- }) |
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+##setReplaceMethod("snpCallProbability", c("CNSet", "ff_or_matrix"), |
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+## function(object, ..., value){ |
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+## assayDataElementReplace(object, "callProbability", value) |
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+## }) |
... | ... |
@@ -1,6 +1,16 @@ |
1 | 1 |
## Need to submit from a fat node! |
2 | 2 |
all: illumina_copynumber copynumber |
3 | 3 |
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+testing: testing.Rnw |
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+ echo "Stangle(\"testing.Rnw\")" | R --no-save --no-restore; |
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+ cat ~/bin/cluster.template | perl -pe "s/Rprog/testing.R/" > testing.R.sh |
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+ qsub -m e -r y -cwd -l mem_free=12G,h_vmem=16G testing.R.sh |
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+ |
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+testingFF: testingFF.Rnw |
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+ echo "Stangle(\"testingFF.Rnw\")" | R --no-save --no-restore; |
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+ cat ~/bin/cluster.template | perl -pe "s/Rprog/testingFF.R/" > testingFF.R.sh |
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+ qsub -m e -r y -cwd -l mem_free=12G,h_vmem=16G testingFF.R.sh |
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+ |
|
4 | 14 |
copynumber: copynumber.Rnw |
5 | 15 |
echo "Stangle(\"copynumber.Rnw\")" | R --no-save --no-restore; |
6 | 16 |
cat ~/bin/cluster.template | perl -pe "s/Rprog/copynumber.R/" > copynumber.R.sh |