extract_ti_from_se: Extract tumor immune quantifications

In federicomarini/quantiseqr: Quantification of the Tumor Immune contexture from RNA-seq data

Extract tumor immune quantifications

Description

Extract tumor immune quantifications from a SummarizedExperiment object, previously processed with run_quantiseqr()

Usage

extract_ti_from_se(se)

Arguments

se	A SummarizedExperiment object, or any of its derivates, which contains the quantifications extracted via quantiseqr in its colData slot.

Value

A data.frame, formatted as required by downstream functions

Examples

data(dataset_racle)
dim(dataset_racle$expr_mat)

# using a SummarizedExperiment object
library("SummarizedExperiment")
se_racle <- SummarizedExperiment(
  assays = List(
    abundance = dataset_racle$expr_mat
  ),
  colData = DataFrame(
    SampleName = colnames(dataset_racle$expr_mat)
  )
)

res_run_SE <- quantiseqr::run_quantiseq(
    expression_data = se_racle,
    signature_matrix = "TIL10",
    is_arraydata = FALSE,
    is_tumordata = TRUE,
    scale_mRNA = TRUE
)

extract_ti_from_se(res_run_SE)

federicomarini/quantiseqr documentation built on May 7, 2024, 9:50 a.m.