camelTest: camelTest - calculating permutation tests for camel measures...

Description Usage Arguments Value Author(s)

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.

Usage

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)

Arguments

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.

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


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