readBam {ORFik} | R Documentation

## Custom bam reader

### Description

Only for single end reads Safer version that handles the most important error done. In the future will use a faster .bam loader for big .bam files in R.

### Usage

    readBam(path, chrStyle = NULL)

### Arguments

`path` | a character path to .bam file
`chrStyle` | a GRanges object, or a `seqlevelsStyle` (Default: NULL) to get seqlevelsStyle from. Is chromosome 1 called chr1 or 1, is mitocondrial chromosome called MT or chrM etc. Will use 1st seqlevel-style if more are present. Like: c("NCBI", "UCSC") -> pick "NCBI"

### Value

a `GAlignments` object of bam file

### See Also

Other utils: `bedToGR()`, `convertToOneBasedRanges()`, `fimport()`, `findFa()`, `fread.bed()`, `optimizeReads()`, `readWig()`

### Examples

    bam_file <- system.file("extdata", "ribo-seq.bam", package = "ORFik")
    readBam(bam_file, "UCSC")

[Package ORFik version 1.6.9 Index]