R: camelTest - calculating permutation tests for camel measures...
camelTest
R Documentation
camelTest - calculating permutation tests for camel measures (sequential and parallel versions)
Description
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.
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.
Value
data frame with p-values of camel tests for all regions, measures and data normalisations specified
Author(s)
Alicja Szabelska, Marek Wiewiorka, Michal Okoniewski