| 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. |