BED file with same genomic coordinates as in BAMs (preferably standard hg19)
iGroup
Name of the attribute/group in the experimental description (i.e. covdesc)
iT1
name of the first group from the experiment (it should be consistent with the groupings specified in covdesc file)
iT2
name of the other group from the experiment (it should be consistent with the groupings specified in covdesc file)
iMeasure
vector specifing camel measures to be calculated
iCovdesc
Covdesc-like data frame - BAM files are read from row names. Similar to covdesc in simpleaffy and rnaSeqMap - tab delimited table of BAM files and groupings. This is the table of experimental design.
iParallel
boolean specifing whether calculations shoulb be run in parallel,true by default,
The degree of parallelism is set up automagically and by default equals to the number of logical CPU cores.
Value
data frame with camel measures calculated for the specified regions and samples
Author(s)
Alicja Szabelska, Marek Wiewiorka, Michal Okoniewski