A container for quantitative DNA sequencing data for ABCD-DNA analyses

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Description

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.

Usage

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

Arguments

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

Details

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.

Value

a QdnaData object (effectively a list) is returned

Author(s)

Mark Robinson

References

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

See Also

getSampleOffsets, plotQdnaByCN, setCNVOffsets

Examples

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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)

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