geneLevelStats {diffUTR} | R Documentation

## geneLevelStats

### Description

Aggregates bin-level statistics to the gene-level

### Usage

    geneLevelStats(
      se,
      coef = NULL,
      excludeTypes = NULL,
      includeTypes = NULL,
      returnSE = TRUE,
      minDensityRatio = 0.1,
      minWidth = 20,
      excludeGeneAmbiguous = TRUE
    )

### Arguments

`se` | A 'RangedSummarizedExperiment' containing the results of one of the DEU wrappers.
`coef` | The coefficients tested (if the model included more than one term).
`excludeTypes` | Vector of bin types to exclude.
`includeTypes` | Vector of bin types to include (overrides 'excludeTypes')
`returnSE` | Logical; whether to return the updated 'se' object (default), or the gene-level table.
`minDensityRatio` | Minimum ratio of read density (with respect to the gene's average) for a bin to be included.
`minWidth` | Minimum bin width to include
`excludeGeneAmbiguous` | Logical; whether to exclude bins which are ambiguous (i.e. can be from different genes)

### Value

If 'returnSE=TRUE' (default), returns the 'se' object with an updated 'metadata(se)$geneLevel' slot, otherwise returns the gene-level data.frame.

### Examples

    library(SummarizedExperiment)
    data(example_bin_se)
    se <- diffSpliceWrapper(example_bin_se, ~condition)
    se <- geneLevelStats(se, includeTypes="3UTR")
    head(metadata(se)$geneLevel)

[Package diffUTR version 1.0.0 Index]