# Copy number analysis of high-throughput sequencing cancer data

## Documentation for package ‘seqCNA’ version 1.40.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## 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.