camelTest {ampliQueso} | 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.

### Usage

    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

[Package ampliQueso version 1.20.0 Index]