prepareBins {diffUTR} | R Documentation

## prepareBins

### Description

prepareBins

### Usage

    prepareBins(
      g,
      APA = NULL,
      onlyMainChr = TRUE,
      removeAntisense = TRUE,
      chrStyle = NULL,
      maxUTRbinSize = 15000,
      codingOnly = FALSE,
      genewise = FALSE,
      stranded = FALSE,
      verbose = TRUE
    )

### Arguments

`g` | A GRanges (or path to RDS file containing a GRanges) or path to a gtf file or EnsDb object containing the gene annotation.
`APA` | A GRanges (or path to a GRanges in RDS format) or bed file containing the alternative poly-A site database
`onlyMainChr` | Logical; whether to keep only main chromosomes
`removeAntisense` | Logical; whether to remove antisense APA sites
`chrStyle` | Chromosome notation to convert to (default no conversion)
`maxUTRbinSize` | Max width of new alternative UTR bins
`codingOnly` | Logical, whether to keep only coding transcripts
`genewise` | Logical, whether annotation should be flattened genewise
`stranded` | Logical, whether to perform disjoin in a stranded fashion.
`verbose` | Logical, whether to print run information

### Details

See the vignette for more details.

### Value

A 'GRanges' object.

### Author(s)

Stefan Greber

### Examples

    data(example_gene_annotation)
    bins <- prepareBins(example_gene_annotation)

[Package diffUTR version 1.0.0 Index]