get_counts: Obtain read counts from 'bam' object.
In asrinivasan-oa/gcount: Obtain Raw Read Counts from RNASeq Data

Description Usage Arguments Value Examples

get_counts allows to obtain read counts quickly and easily from RNASeq data to be used in downstream analyses.

get_counts(reads, annotation, transcript_id = "transcript_id",
  gene_id = "gene_id", mismatches = -1L, minoverlap = 1L,
  feature = c("gene_exon", "gene", "exon", "intron"), type = c("default",
  "union", "disjoin", "intersect", "longest", "shortest", "overlap"),
  library = c("unstranded", "firststrand", "secondstrand"), paired = FALSE,
  multiple_feature_overlaps = FALSE, verbose = FALSE)

`reads`	A `bam/bed` object (see `gread::read_format`) or complete path to a `bam/bed` file.
`annotation`	A `gtf/gff` object (see `gread::read_format`) or complete path to `gtf/gff` file.
`transcript_id`	Column name in `x` corresponding to transcript id. Default value is `"transcript_id"`.
`gene_id`	Column name in `x` corresponding to gene id. Default value is `"gene_id"`.
`mismatches`	Default `-1` is to ignore mismatches. If `> 0`, reads with mismatches `<= mismatches` are alone retained.
`minoverlap`	Argument that's passed to `GenomicRanges::findOverlaps`. Default is `1L`, i.e., select all overlapping reads.
`feature`	How to count reads? `"gene_exon"` counts only exonic reads within genes. `"gene"` counts any/all reads overlapping the gene. `"exon"` returns read counts for each exon separately. `"intron"` returns read counts for each intron separately. See `type` argument for more advanced operations on extracting feature coordinates.
`type`	Same as `gread::extract`. See `?extract` in `gread`.
`library`	Either `"unstranded"` (default), `"firststrand"` or `"secondstrand"`.
`paired`	Default is `FALSE`. If the library is `paired end`, set it to `TRUE`
`multiple_feature_overlaps`	logical. Should reads that overlap multiple features be counted. Default is `FALSE`, i.e., to discard. If `TRUE`, reads across overlapping features will be counted.
`verbose`	logical. Default is `FALSE`. If `TRUE`, provides helpful messages to the console.

A data.table with calculated raw counts of overlapping reads for each feature.

path <- system.file("tests", package="gcount")
gtf_file <- file.path(path, "sample.gtf")
bam_file <- file.path(path, "sample.bam")
bam_counts <- get_counts(bam_file, gtf_file, feature="gene_exon", 
             type="union", paired=FALSE, library="unstranded", 
             verbose=TRUE)