annotateGenes |
annotateGenes Annotate genes with genomic coordinates with reference to hg38 using Ensembl based annotation package |
classifyCluster |
classifyCluster Classify the two major clusters of CNA matrix on the basis of confident normal cells |
classifyTumorCells |
classifyTumorCells Classify tumour and normal cells from the raw count matrix, using normal cells in the matrix or by subtracting a synthetic baseline from the matrix if there are no normal cells in the matrix. |
computeCNAmtx |
computeCNAmtx computed the CNA matrix using the break points obtained from segmentation |
getConfidentNormalCells |
getConfidentNormalCells Get at most top 30 confident normal cells from count matrix. |
pipelineCNA |
pipelineCNA Executes the entire SCEVAN pipeline that classifies tumour and normal cells from the raw count matrix, infer the clonal profile of cancer cells and looks for possible sub-clones in the tumour cell matrix automatically analysing the specific and shared alterations of each subclone and a differential analysis of pathways and genes expressed in each subclone. |
removeSyntheticBaseline |
removeSyntheticBaseline Removes a synthetic baseline from a tumour pure matrix |
sortData |
This function sorts a dataset file by the genomic position of the probes. |
top30classification |
Get at most top 30 confident normal cells |