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seqCNA (version 1.18.0)

Copy number analysis of high-throughput sequencing cancer data

Description

Copy number analysis of high-throughput sequencing cancer data with fast summarization, extensive filtering and improved normalization

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Version

Version

1.18.0

License

GPL-3

Maintainer

David MosenAnsorena

Last Published

February 15th, 2017

Functions in seqCNA (1.18.0)

runGLAD

Wrapper function that runs the GLAD segmentation algorithm on a SeqCNAInfo-class object.
readSeqsumm

Function that reads seqsumm summarized files.
applyFilters

The function applies a set of filters to the raw profile.
seqsumm_HCC1143

Example of a seqsumm output, namely for a sequenced sample of the HCC1143 cancer cell-line.
runSeqnorm

This function calls seqnorm, which normalizes the tumoural profile with respect to either a paired sample or GC content.
applyThresholds

Apply thresholds on the segmented profile in order to call copy numbers.
SeqCNAInfo-class

Class "SeqCNAInfo"
plotCNProfile

Plots the profile of a SeqCNAInfo-class object.
seqCNA-package

Copy number analysis of deep sequencing cancer data
runSeqsumm

Function that generates seqsumm summarized files.
writeCNProfile

Outputs the processed profile of a SeqCNAInfo-class object to the specified folder.