immunedeconv (version 0.1.1)

deconvolute: Perform an immune cell deconvolution on a dataset.

Description

Perform an immune cell deconvolution on a dataset.

Usage

deconvolute.default(gene_expression, method = deconvolution_methods,
  indications = NULL, tumor = TRUE, arrays = FALSE)
deconvolute(gene_expression, method = deconvolution_methods,
  column = "gene_symbol", indications = NULL)
# S4 method for eSet,character,character,character
deconvolute(gene_expression,
  method = deconvolution_methods, column = "gene_symbol",
  indications = NULL)
# S4 method for eSet,character,character,missing
deconvolute(gene_expression,
  method, column = "gene_symbol")
# S4 method for matrix,character,missing,character
deconvolute(gene_expression,
  method, indications = NULL)
# S4 method for matrix,character,missing,missing
deconvolute(gene_expression,
  method)
# S4 method for data.frame,character,missing,character
deconvolute(gene_expression,
  method, indications = NULL)
# S4 method for data.frame,character,missing,missing
deconvolute(gene_expression,
  method)

Arguments

gene_expression

A numeric matrix with HGNC gene symbols as rownames and sample identifiers as colnames. Data must be on non-log scale.

method

a string specifying the method. Supported methods are xcell, ...

indications

a character vector with one indication per sample for TIMER. Argument is ignored for all other methods.

tumor

use a signature matrix/procedure optimized for tumor samples, if supported by the method. Currently affects EPIC and quanTIseq.

arrays

Runs methods in a mode optimized for microarray data. Currently affects quanTIseq and CIBERSORT.

...

arguments passed to the respective method

eset

Expression set

col

column name of the fData column that contains HGNC gene symbols.

Value

data.frame with cell_type as first column and a column with the calculated cell fractions for each sample.

Methods (by class)

• gene_expression = eSet,method = character,column = character,indications = character: eset is a Biobase::ExpressionSet. fData contains a column with HGNC gene symbols (specify column name)

• gene_expression = eSet,method = character,column = character,indications = missing: variant where indications are not defined, cannot be used with method == 'timer'

• gene_expression = matrix,method = character,column = missing,indications = character: matrix is matrix with HGNC gene symbols as row names.

• gene_expression = matrix,method = character,column = missing,indications = missing: variant where indications are not defined, cannot be used with method=='timer'

• gene_expression = data.frame,method = character,column = missing,indications = character: matrix is data frame with HGNC gene symbols as row names.

• gene_expression = data.frame,method = character,column = missing,indications = missing: variant where indications are not defined, cannot be used with method=='timer'

Examples

# NOT RUN {
# Not run: deconvolute(gene_expression_matrix, "xcell")

# }