SCEVAN


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Documentation for package ‘SCEVAN’ version 1.0.1

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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