Copy number analysis of high-throughput sequencing cancer data

Documentation for package ‘seqCNA’ version 1.34.0

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.