calcCounts {MDTS} | R Documentation |
This function will return a matrix of read counts where ecah column is a sample, and each row is a bin.
calcCounts(metaData, bins, rl, mc.cores = 1)
metaData |
A table in the format of the output of getMetaData(). |
bins |
The set of bins determined by calcBins(). |
rl |
The read length of the experiment. |
mc.cores |
The number of cores to use for multi-threaded analysis. Defaults to 1. |
A data.frame
that contains the counts for each sample in the
metaData
input that fall into each segment of bins
.
## Not run: pD <- getMetaData( 'https://raw.githubusercontent.com/JMF47/MDTSData/master/data/pD.ped') genome = BSgenome.Hsapiens.UCSC.hg19 map_file <- "https://raw.githubusercontent.com/JMF47/MDTSData/master/data/chr1.map.bw" bins = calcBins(pD, n=5, rl=100, med=150, min=5, genome, map_file) ## End(Not run) load(system.file("extdata", 'bins.RData', package = "MDTS")) load(system.file("extdata", 'counts.RData', package = "MDTS")) counts