fimport {ORFik} | R Documentation

## Load any type of sequencing reads

### Description

Wraps around rtracklayer::import and tries to speed up loading with the use of data.table. Supports gzip, gz, bgz compression formats. Also safer chromosome naming with the argument chrStyle

### Usage

    fimport(path, chrStyle = NULL)

### Arguments

`path` | a character path to file or a GRanges/Galignment object etc. Any Ranged object.
`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"

### Details

NOTE: For wig you can send in 2 files, so that it automaticly merges forward and reverse stranded objects. You can also just send 1 wig file, it will then have "*" as strand.

### Value

a `GAlignments`/`GRanges` object, depending on input.

### See Also

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

### Examples

    bam_file <- system.file("extdata", "ribo-seq.bam", package = "ORFik")
    fimport(bam_file)
    # Certain chromosome naming
    fimport(bam_file, "NCBI")

[Package ORFik version 1.6.9 Index]