Call aberrations in segmented data
Segments, obtained by pcf or multipcf, are classified as "gain", "normal" or "loss" given the specified thresholds.
callAberrations(segments, thres.gain, thres.loss = -thres.gain)
segments |
a data frame containing the segmentation results found by either |
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 |
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.
A new segment data frame where the segment values have been replaced by the classification "gain", "normal" or "loss".
Gro Nilsen
#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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