plotQdnaByCN {Repitools} | R Documentation

## 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)

[Package Repitools version 1.38.0 Index]