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

In markrobinsonuzh/Repitools: Epigenomic tools

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

Author(s)

Mark Robinson

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)

markrobinsonuzh/Repitools documentation built on March 20, 2024, 6:04 a.m.