camelTest {ampliQueso} | R Documentation |
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.
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. |
data frame with p-values of camel tests for all regions, measures and data normalisations specified
Alicja Szabelska, Marek Wiewiorka, Michal Okoniewski