Repitools (version 1.18.0)

getSampleOffsets: Calculates the sample-specific offsets, using the neutral state

Description

ABCD-DNA combines CNV offsets with sample specific factors. This function calculates the latter, using a set of neutral regions (and corresponding counts in the count table).

Usage

getSampleOffsets(obj, ref = 1, quantile = 0.99, min.n = 100, plot.it = FALSE, force = FALSE, ...)

Arguments

obj

a QdnaData object

ref

integer index, giving the sample to use as reference

quantile

quantile of the A-values to use

min.n

minimum number of points to include

plot.it

logical, whether to plot an M-A plot for each sample against the reference (default: FALSE)

force

logical, whether to recalculate the sample-specific offsets (only needed if they are already calculated)

...

arguments to pass to the maPlot function

Value

returns a QdnaData object (copied from the obj argument) and populates the $DGEList$samples$norm.factors element and sets the $sample.specific.calculated to TRUE.

Details

The sample-specific offset is calculated as the median M-value beyond (i.e. to the right) an A-value quantile, using only the copy-number-neutral regions, as specified in the incoming QdnaData object.

References

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

See Also

QdnaData

Examples

# library(Repitools)
# qd <- QdnaData(counts=counts, regions=gb, design=design, 
#               cnv.offsets=cn, neutral=(regs=="L=4 P=2"))
# qd <- getSampleOffsets(qd,ref=1)