quanTIseq {quantiseqr} | R Documentation |
Run quanTIseq deconvolution
quanTIseq(currsig, currmix, scaling = TRUE, method = "lsei")
currsig |
Signature matrix to be used for deconvolution (format: genes by cell types). |
currmix |
Mixture matrix to be deconvoluted (format: genes by samples). |
scaling |
Logical value. If set to FALSE, it disables the correction of cell-type-specific mRNA content bias. Default: TRUE |
method |
Character string, defining the deconvolution method to be used:
|
A data.frame of cell fractions, cell types by samples.
data(dataset_racle) mixture <- dataset_racle$expr_mat signature.file <- system.file( "extdata", "TIL10_signature.txt", package = "quantiseqr", mustWork = TRUE) signature <- read.table(signature.file, header = TRUE, sep = "\t", row.names = 1) # cellfrac <- quantiseqr:::quanTIseq(mixture, signature)