compareCoveragesReg {ampliQueso} | R Documentation

## compareCoveragesReg - calculating given camel measures for a list of regions specified by a BED file (sequential and parallel versions)

### Description

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

### Usage

    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

[Package ampliQueso version 1.18.0 Index]