extract_ti_from_se {quantiseqr} | R Documentation

## 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)

[Package quantiseqr version 1.2.0 Index]