create_sig_matrix: create a signature matrix for usage with CIBERSORT or...

In MarianSchoen/DMC: Comparison of different Deconvolution Models in several scenarios

create a signature matrix for usage with CIBERSORT or DeconRNASeq according to description in Newman et. al

Description

create a signature matrix for usage with CIBERSORT or DeconRNASeq according to description in Newman et. al

Usage

create_sig_matrix(
  exprs,
  pheno,
  exclude.celltypes = NULL,
  max.genes = NULL,
  cell.type.column = "cell_type"
)

Arguments

exprs	non-negative numeric matrix,
pheno	data.frame, phenodata corresponding to expression data, same ordering of samples/cells; cell type label column must be named 'cell.type.column'
exclude.celltypes	character vector, defaults to c("malignant", "not_annotated", "unassigned"). Cells with these labels are not included in the signature matrix
max.genes	integer, maximum number of genes to be selected for each cell type; the actual number of genes in the signature matrix will be larger. If no value is given, max.genes = NULL and all genes will be selected as maximum
cell.type.column	string, which column of 'pheno' holds the cell type information? default "cell_type"

Value

numeric matrix, holding reference profiles in its column, features in its rows

MarianSchoen/DMC documentation built on Aug. 2, 2022, 3:05 p.m.