| 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