controlQC: Boxplots of control and non-control probes

In charm: Analysis of DNA methylation data from CHARM microarrays

Description

Make boxplots of the non-control probes and the control probes (after spatial and background correction but before any normalization), to confirm that the control probes have a lower distribution of intensities than the non-control probes.

Usage

controlQC(rawData, controlProbes=NULL, controlIndex=NULL, IDcol, expcol, ylimits=c(-6,8), outfile="./boxplots_check.pdf", height=7, width=9) 

Arguments

rawData	a TilingFeatureSet object
controlProbes	character string of the label assigned to non-CpG control probes in the annotation file (i.e. the container column of the .ndf file) (getContainer reports the container values for the pm probes). This is used only if controlIndex is not provided. Either this or controlIndex must be provided.
controlIndex	a vector of non-CpG control probe indices (can be obtained using getControlIndex). Either this or controlProbes must be provided.
IDcol	column name of pData(rawData) with which to label samples in the output plot.
expcol	name of the column of pData(rawData) by which to order and, if not numeric, color the boxes.
ylimits	ylim argument to plot()
outfile	file argument to pdf()
height	height argument to pdf()
width	width argument to pdf()

Value

A data frame with one row per sample and columns

non_control

Median methylation value among the non-control probes

control

Median methylation value among the control probes

diff

non_control-control

Author(s)

Martin Aryee <[e-mail]>, Peter Murakami, Rafael Irizarry

See Also

regionPlot, dmrFinder, dmrFdr

Examples

# See dmrFdr

charm documentation built on May 6, 2019, 2:29 a.m.