QdnaData: A container for quantitative DNA sequencing data for ABCD-DNA...
In Repitools: Epigenomic tools

Description Usage Arguments Details Value Author(s) References See Also Examples

QdnaData objects form the basis for differential analyses of quantitative DNA sequencing data(i.e. ABCD-DNA). A user is required to specify the minimum elements: a count table, a list of regions and a design matrix. For copy-number-aware analyses, a table of offsets and the set of neutral regions needs to be given.

1	QdnaData(counts, regions, design, cnv.offsets = NULL, neutral = NULL)

`counts`	table of counts for regions of interest across all samples
`regions`	a `GRanges` object giving the regions
`design`	a design matrix
`cnv.offsets`	a table of offsets. If unspecified (or `NULL`), a matrix of 1s (i.e. no CNV) is used
`neutral`	a logical vector, or indices, of the regions deemed to be neutral. If unspecified (or `NULL`), all regions are used

QdnaData objects are geared for general differential analyses of qDNA-seq data. If CNV is present and prominent, the objects and methods available with QdnaData perform adjustments and spot checks before the differential analysis.

a QdnaData object (effectively a list) is returned

Mark Robinson

http://imlspenticton.uzh.ch/robinson_lab/ABCD-DNA/ABCD-DNA.html

getSampleOffsets, plotQdnaByCN, setCNVOffsets

require(GenomicRanges)
cnt <- matrix(rpois(20,lambda=10),ncol=4)
gr <- GRanges("chr1",IRanges(seq(2e3,6e3,by=1e3), width=500))
des <- model.matrix(~c(0,0,1,1))
qd <- QdnaData( counts=cnt, regions=gr, design=des)