extract_ti_from_se {quantiseqr} | R Documentation |
Extract tumor immune quantifications from a SummarizedExperiment object,
previously processed with run_quantiseqr()
extract_ti_from_se(se)
se |
A |
A data.frame, formatted as required by downstream functions
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)