Compute the pairwise correlations between individual cells' CNA values and the average CNA values in their tumour of origin.
cnaCor(cna, cor.method = "pearson", threshold = NULL, bySample = F, samples = NULL, sep = "-|_", excludeFromAvg = NULL)
| cna | a matrix of gene rows by cell columns containing CNA values. |
|---|---|
| cor.method | character string indicating the method to use for the pairwise correlations. E.g. 'pearson', 'spearman'. Default: 'pearson' |
| samples | a character vector of sample names list of character vectors (cell/column names). Can be provided if the cna matrix contains multiple samples of cells, i.e. multiple tumours, such that the cell-group correlations are calcualted for each group/tumour in turn. Default: FALSE |
| sep | if bySample is TRUE and samples are NULL, split cell IDs by <sep> and take the first substring to be the sample name. Default: '-|_' |
a numeric vector or list of numeric vectors