QdnaData {Repitools} | R Documentation

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

### 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

    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

    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)

[Package Repitools version 1.28.0 Index]