import-functions {BRGenomics} | R Documentation

## Import basepair-resolution files

### Description

Import functions for plus/minus pairs of `bigWig` or `bedGraph` files.

### Usage

    import_bigWig(
      plus_file = NULL,
      minus_file = NULL,
      genome = NULL,
      keep.X = TRUE,
      keep.Y = TRUE,
      keep.M = FALSE,
      keep.nonstandard = FALSE,
      makeBRG = TRUE,
      ncores = getOption("mc.cores", 2L)
    )

    import_bedGraph(
      plus_file = NULL,
      minus_file = NULL,
      genome = NULL,
      keep.X = TRUE,
      keep.Y = TRUE,
      keep.M = FALSE,
      keep.nonstandard = FALSE,
      ncores = getOption("mc.cores", 2L)
    )

### Arguments

`plus_file, minus_file` | Paths for strand-specific input files, or a vector of such paths. If vectors are given, the user should take care that the orders match!
`genome` | Optional string for UCSC reference genome, e.g. "hg38". If given, non-standard chromosomes are trimmed, and options for sex and mitochondrial chromosomes are applied.
`keep.X, keep.Y, keep.M, keep.nonstandard` | Logicals indicating which non-autosomes should be kept. By default, sex chromosomes are kept, but mitochondrial and non-standard chromosomes are removed.
`makeBRG` | If `TRUE` (the default), the output ranges are made single-width using `makeGRangesBRG`
`ncores` | Number of cores to use, if importing multiple objects simultaneously.

### Details

For `import_bigWig`, the output GRanges is formatted by `makeGRangesBRG`, such that all ranges are disjoint and have width = 1, and the `score` is single-base coverage, i.e. the number of reads for each position.

`import_bedGraph` is useful for when both 5'- and 3'-end information is to be maintained for each sequenced molecule. For this purpose, one use bedGraphs to store entire reads, with the `score` representing the number of reads sharing identical 5' and 3' ends. However, `import_bedGraph` doesn't modify the information in the bedGraph files. If the bedGraph file represents basepair-resolution coverage data, then users can coerce it to a basepair-resolution GRanges object by using `getStrandedCoverage` followed by `makeGRangesBRG`.

### Value

Imports a GRanges object containing base-pair resolution data, with the `score` metadata column indicating the number of reads represented by each range.

### Author(s)

Mike DeBerardine

### See Also

`tidyChromosomes`, `rtracklayer::import`

### Examples

    #--------------------------------------------------#
    # Import PRO-seq bigWigs -> coverage of 3' bases
    #--------------------------------------------------#

    # get local address for included bigWig files
    p.bw <- system.file("extdata", "PROseq_dm6_chr4_plus.bw",
                        package = "BRGenomics")
    m.bw <- system.file("extdata", "PROseq_dm6_chr4_minus.bw",
                        package = "BRGenomics")

    # import bigWigs (not supported on windows)
    if (.Platform$OS.type == "unix") {
        PROseq <- import_bigWig(p.bw, m.bw, genome = "dm6")
        PROseq
    }

    #--------------------------------------------------#
    # Import PRO-seq bedGraphs -> whole reads (matched 5' and 3' ends)
    #--------------------------------------------------#

    # get local address for included bedGraph files
    p.bg <- system.file("extdata", "PROseq_dm6_chr4_plus.bedGraph",
                        package = "BRGenomics")
    m.bg <- system.file("extdata", "PROseq_dm6_chr4_minus.bedGraph",
                        package = "BRGenomics")

    # import bedGraphs
    PROseq_paired <- import_bedGraph(p.bg, m.bg, genome = "dm6")
    PROseq_paired

[Package BRGenomics version 1.0.3 Index]