* collab:
update Rds
revert imputeGender to original api
bug fix for calculateRBafCNSet
update calculateRBafCNSet
Fix documentation for crlmmCopynumber -- added argument fitLinearModel
update crlmmGT2
Put rm(DD, ...) further down in crlmmGT2 function
remove message about cloning A and B
Open and close callsPr and callsGt in crlmmGT2 (when args not missing)
revert removed indices loaded in crlmmGT2
snprmaAffy no longer writes normalized intensities to calls and callProbability slots. crlmmGT2 takes arguments callsGt and callsPr. When present, crlmmGT2 will not overwrite A and B.
explicit coercion to matrix in imputeGender
Assign imputed gender to cnSet$gender within crlmmGT2 function.
Change sum(SNR > SNRmin) to sum(SNR[] > SNRmin) in imputeGender
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@69450 bc3139a8-67e5-0310-9ffc-ced21a209358
Rob Scharp authored on 14/09/2012 20:07:37
| 1 | 1 |
new file mode 100644 |
| ... | ... |
@@ -0,0 +1,44 @@ |
| 1 |
+\name{constructAffyCNSet}
|
|
| 2 |
+\alias{constructAffyCNSet}
|
|
| 3 |
+ |
|
| 4 |
+\title{ Construct an object of class CNSet from Affymetrix cel files
|
|
| 5 |
+} |
|
| 6 |
+\description{
|
|
| 7 |
+Construct a container for normalized intensities for Affymetrix cel |
|
| 8 |
+files, referred to as a \code{CNSet}
|
|
| 9 |
+} |
|
| 10 |
+\usage{
|
|
| 11 |
+constructAffyCNSet(filenames, sns, cdfName, batch, verbose = TRUE, genome) |
|
| 12 |
+} |
|
| 13 |
+%- maybe also 'usage' for other objects documented here. |
|
| 14 |
+\arguments{
|
|
| 15 |
+ \item{filenames}{
|
|
| 16 |
+ Vector of cel file names. |
|
| 17 |
+} |
|
| 18 |
+ \item{sns}{
|
|
| 19 |
+ Sample identifiers. Defaults to \code{basename(filenames)}.
|
|
| 20 |
+} |
|
| 21 |
+ \item{cdfName}{
|
|
| 22 |
+ Character string indicating annotation package (e.g., "genomewidesnp6Crlmm") |
|
| 23 |
+} |
|
| 24 |
+ \item{batch}{
|
|
| 25 |
+ Vector of same length as filenames indicating batch. |
|
| 26 |
+} |
|
| 27 |
+ \item{verbose}{
|
|
| 28 |
+ Logical. |
|
| 29 |
+} |
|
| 30 |
+ \item{genome}{
|
|
| 31 |
+ Character string indicating UCSC genome build (hg18 or hg19 supported) |
|
| 32 |
+} |
|
| 33 |
+} |
|
| 34 |
+ |
|
| 35 |
+\value{
|
|
| 36 |
+ An object of class \code{CNSet}
|
|
| 37 |
+} |
|
| 38 |
+ |
|
| 39 |
+\author{
|
|
| 40 |
+R. Scharpf |
|
| 41 |
+} |
|
| 42 |
+% Add one or more standard keywords, see file 'KEYWORDS' in the |
|
| 43 |
+% R documentation directory. |
|
| 44 |
+\keyword{manip}
|
|
| 0 | 45 |
\ No newline at end of file |