plotQdnaByCN: Plotting the response of qDNA-seq data by CNV
In Repitools: Epigenomic tools

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

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.

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

`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`

a plot to the current graphics device

Mark Robinson

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

QdnaData, ~~~

# 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)

Repitools documentation built on Nov. 8, 2020, 7:52 p.m.