computeGC-methods {ArrayTV} | R Documentation |
Compute the GC composition for selected windows around a vector of genomic positions (e.g., locations of markers on an array)
computeGC(x, maxwins, increms, chr, build, ...)
:
x
can be numeric, in which case x
should be a vector
of physical position along the genome. Alternatively, x
can be an instance of the BafLrrSetList
class. When
x
is numeric
, arguments chr
and build
are required. Arguments chr
and build
are ignored
for BafLrrSetList
objects.
Arguments maxwins
, increms
, build
, and
chr
are as described in the documentation for
gcCorrectMain
if(require(crlmm) && require(ff) && require(doParallel)){ ## nodes may be set to the number of cpus available nodes<-3 cl <- makeCluster(nodes) registerDoParallel(cl) data(cnSetExample, package="crlmm") brList <- BafLrrSetList(cnSetExample) pos <- unlist(position(brList)) chr <- paste("chr", rep(chromosome(brList), elementNROWS(brList)), sep="") gc.matrix1 <- ArrayTV:::computeGC(x=pos, maxwins=c(12,10e3), increms=c(12,10e3), chr=chr, build="hg19") gc.matrix2 <- ArrayTV:::computeGC(brList, c(12, 10e3), c(12, 10e3)) identical(gc.matrix1, gc.matrix2) stopCluster(cl) }