camelTest: camelTest - calculating permutation tests for camel measures...
In ampliQueso: Analysis of amplicon enrichment panels

Description Usage Arguments Value Author(s)

Calculating permutation tests for reads coverage (camel) measures for regions specified by a BED file. This function features a few normalization modes and camel measures.

1	camelTest(iBedFile, iCovdesc = "covdesc", iT1, iT2, iNorm = c("none", "density", "minMax"), iMeasure = c("DA", "QQ", "PP", "HD1", "HD2"), iSizes = NULL, iNPerm = 100,iParallel=TRUE)

`iBedFile`	BED file with genomic coordinates refering to the same genome as the BAMs
`iCovdesc`	Covdesc-like file - 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.
`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)
`iNorm`	vector specifing the data normalisations prior to camel measures calculations
`iMeasure`	camel measure to be used in the non-parametric test. Camel measures are implemented in the package rnaSeqMap and described in Okoniewski et al, NAR, 2011
`iSizes`	TBD
`iNPerm`	integer number specifing the number of permutations for camel tests calcualtions
`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.