Copy number analysis of high-throughput sequencing cancer data


[Up] [Top]

Documentation for package ‘seqCNA’ version 1.32.0

Help Pages

seqCNA-package Copy number analysis of deep sequencing cancer data
applyFilters The function applies a set of filters to the raw profile.
applyThresholds Apply thresholds on the segmented profile in order to call copy numbers.
plotCNProfile Plots the profile of a 'SeqCNAInfo-class' object.
readSeqsumm Function that reads seqsumm summarized files.
runGLAD Wrapper function that runs the GLAD segmentation algorithm on a 'SeqCNAInfo-class' object.
runSeqnorm This function calls seqnorm, which normalizes the tumoural profile with respect to either a paired sample or GC content.
runSeqsumm Function that generates seqsumm summarized files.
seqCNA Copy number analysis of deep sequencing cancer data
SeqCNAInfo-class Class '"SeqCNAInfo"'
seqsumm_HCC1143 Example of a seqsumm output, namely for a sequenced sample of the HCC1143 cancer cell-line.
summary-method Class '"SeqCNAInfo"'
writeCNProfile Outputs the processed profile of a 'SeqCNAInfo-class' object to the specified folder.