tableAUC {TBSignatureProfiler} | R Documentation

## Create a table of results for t-tests and bootstrapped AUCs for multiple scored signatures.

### Description

This function collects the results of bootstrapping and t-tests for a scored gene expression dataset and presents them using a JavaScript table with an R interface, or as a `data.frame`.

### Usage

    tableAUC(
      SE_scored,
      annotationColName,
      signatureColNames,
      num.boot = 100,
      pb.show = TRUE,
      output = "DataTable",
      pROC = TRUE
    )

### Arguments

`SE_scored` | a `SummarizedExperiment` object with genes as the row features and signature scores in the `colData`. There should also be a column of annotation data. Required.
`annotationColName` | a character string giving the column name in `colData` that contains the annotation data. Required.
`signatureColNames` | a vector of column names in the `colData` that contain the signature score data. Required.
`num.boot` | integer. The number of times to bootstrap the data. The default is `100`.
`pb.show` | logical for whether to show a progress bar while running code. The default is `TRUE`.
`output` | a character string indicating the table output format. Possible values are `DataTable` and `data.frame`. The default is `DataTable`.
`pROC` | logical. Should pROC AUC confidence intervals be used? Default is `TRUE`.

### Value

A JavaScript table with an R interface using the `DT` package.

### Examples

    # Run signature profiling
     choose_sigs <- TBsignatures[c(1, 2)]
     prof_indian <- runTBsigProfiler(TB_indian, useAssay = "logcounts",
                                     algorithm = "ssGSEA",
                                     signatures = choose_sigs,
                                     parallel.sz = 1)
     # Create table
     tableAUC(SE_scored = prof_indian, annotationColName = "label",
              signatureColNames = names(choose_sigs))

     # Create data.frame object
    h <-  tableAUC(SE_scored = prof_indian, annotationColName = "label",
                   signatureColNames = names(choose_sigs),
                   output = "data.frame",
                   num.boot = 5)
    head(h)

[Package TBSignatureProfiler version 1.4.11 Index]