QdnaData: A container for quantitative DNA sequencing data for ABCD-DNA...

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

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

1
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

1
2
3
4
5
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)


Search within the Repitools package
Search all R packages, documentation and source code

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.