deconvo_quantiseq | R Documentation |
This function performs deconvolution of the tumor microenvironment using the quanTIseq technique. It estimates the fraction of different cell types in the expression dataset.
deconvo_quantiseq(eset, project = NULL, tumor, arrays, scale_mrna)
eset |
gene expression data |
project |
default is NULL, project name used to distinguish different data sets |
tumor |
logistic variable |
arrays |
logistic variable, is data generated from microarray |
scale_mrna |
logistic variable |
A data frame with the estimated cell type fractions, with columns named according to the cell types and suffixed with "_quantiseq".
#' # Loading TCGA-STAD expresion data(raw count matrix)
data(eset_stad, package = "IOBR")
eset <- count2tpm(countMat = eset_stad, source = "local", idType = "ensembl")
deconvo_quantiseq(eset = eset, project = "stad", tumor = TRUE, arrays = FALSE, scale_mrna = FALSE)
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