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charm (version 2.18.0)

controlQC: Boxplots of control and non-control probes

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

See Also

regionPlot, dmrFinder, dmrFdr

Examples

Run this code
# See dmrFdr

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