compareCoveragesReg: compareCoveragesReg - calculating given camel measures for a...

Description Usage Arguments Value Author(s)

Description

Calculating given camel measures for a list of regions specified by a BED file (sequential version)

Usage

1
compareCoveragesReg(iBedFile, iGroup, iT1, iT2, iMeasure = c("DA", "QQ", "PP", "HD1", "HD2"), iCovdesc = "covdesc",iParallel=TRUE)

Arguments

iBedFile

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


ampliQueso documentation built on May 2, 2019, 12:45 a.m.