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. |