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copynumber (version 1.12.0)

callAberrations: Call aberrations in segmented data

Description

Segments, obtained by pcf or multipcf, are classified as "gain", "normal" or "loss" given the specified thresholds.

Usage

callAberrations(segments, thres.gain, thres.loss = -thres.gain)

Arguments

segments
a data frame containing the segmentation results found by either pcf or multipcf.
thres.gain
a numeric value giving the threshold to be applied for calling gains.
thres.loss
a numeric value giving the threshold to be applied for calling losses. Default is to use the negative value of thres.gain.

Value

  • A new segment data frame where the segment values have been replaced by the classification "gain", "normal" or "loss".

Details

Each region found in segments is classified as "gain", "normal" or "loss". Regions with gain or loss will be those segments where the segment value is above or below the value given in thres.gain or thres.loss, respectively.

Examples

Run this code
#load lymphoma data
data(lymphoma)
#Run pcf
seg <- pcf(data=lymphoma,gamma=12)

#Call gains as segments whose value is > 0.2, and losses as segments whose
# value < -0.1
ab.seg <- callAberrations(seg,thres.gain=0.2,thres.loss=-0.1)

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