Deconvolve Using quanTIseq — deconvo

quanTIseq deconvolution for RNA-seq immune cell fractions.

Usage

deconvo_quantiseq(eset, project = NULL, tumor, arrays, scale_mrna)

Arguments

eset: Gene expression matrix.
project: Optional project name. Default is `NULL`.
tumor: Logical: tumor samples. Must be specified.
arrays: Logical: microarray data. Must be specified.
scale_mrna: Logical: correct for mRNA content. Must be specified.

Value

Data frame with quanTIseq cell fractions. Columns suffixed with `_quantiseq`.

Author

Dongqiang Zeng

Examples

if (FALSE) { # \dontrun{
quantiseq_data <- load_data("quantiseq_data")
if (!is.null(quantiseq_data)) {
  set.seed(123)
  n_sig <- nrow(quantiseq_data$TIL10_signature)
  sim_eset <- matrix(rnorm(n_sig * 2), n_sig, 2)
  rownames(sim_eset) <- rownames(quantiseq_data$TIL10_signature)
  colnames(sim_eset) <- paste0("Sample", 1:2)
  result <- deconvo_quantiseq(eset = sim_eset, project = "Example", tumor = TRUE,
                              arrays = FALSE, scale_mrna = FALSE)
  if (!is.null(result)) head(result)
}
} # }