# R: SCEVAN

# SCEVAN

## Documentation for package ‘SCEVAN’ version 1.0.3

- DESCRIPTION file.

## Help Pages

SCEVAN-package | SCEVAN: R package that automatically classifies the cells in the scRNA data by segregating non-malignant cells of tumor microenviroment from the malignant cells. It also infers the copy number profile of malignant cells, identifies subclonal structures and analyses the specific and shared alterations of each subpopulation.
annotateGenes | annotateGenes Annotate genes with genomic coordinates with reference to hg38 using Ensembl based annotation package
annoteBandOncoHeat | annoteBandOncoHeat Annotate with chromosome bands the data frame with difference copy number alterations between subclones
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
getBreaksVegaMC | getBreaksVegaMC Get SCEVAN segmentation of the matrix.
getConfidentNormalCells | getConfidentNormalCells Get at most top 30 confident normal cells from count matrix.
multiSampleComparisonClonalCN | multiSampleComparisonClonalCN Compare the clonal Copy Number of multiple samples.
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.
plotAllClonalCN | Title plotAllClonalCN
plotAllSubclonalCN | plotAllSubclonalCN Plot the copy number of each subclone of a sample.
plotCNA_withAnnotCells | plotCNA_withAnnotCells allows generating a heatmap of the copy number profile of each cell, adding cell annotations as tracks on the heatmap.
removeSyntheticBaseline | removeSyntheticBaseline Removes a synthetic baseline from a tumour pure matrix
SCEVAN | SCEVAN: R package that automatically classifies the cells in the scRNA data by segregating non-malignant cells of tumor microenviroment from the malignant cells. It also infers the copy number profile of malignant cells, identifies subclonal structures and analyses the specific and shared alterations of each subpopulation.
sortData | This function sorts a dataset file by the genomic position of the probes.
top30classification | Get at most top 30 confident normal cells