Repitools (version 1.18.0)

plotQdnaByCN: Plotting the response of qDNA-seq data by CNV

Description

Given groupings of relative CNV state, this function produces M-A (log-fold-change versus log-average) plots to compare two samples relative read densities. In addition, it calculates a scaling factor at a specified quantile and plots the median M value across all the groups.

Usage

plotQdnaByCN(obj, cnv.group, idx.ref = 1, idx.sam = 2, min.n = 100, quantile = 0.99, ylim = c(-5, 5), ...)

Arguments

obj

a QdnaData object

cnv.group

a character vector or factor giving the relative CNV state. This must be the same length as the number of regions in obj

idx.ref

index of the reference sample (denominator in the calculation of M values)

idx.sam

index of the sample of interest (numerator in the calculation of M values)

min.n

minimum number of points to include

quantile

quantile of the A-values to use

ylim

y-axis limits to impose on all M-A plots

...

further arguments sent to maPlot

Value

a plot to the current graphics device

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"))
# plotQdnaByCN(qd,cnv.group=regs,idx.ref=3,idx.sam=2)