outputLibs {ORFik} | R Documentation

## Output bam/bed/bedo/wig files to R as variables

### Description

Variable names defined by df (ORFik experiment DataFrame) Uses multiple cores to load, defined by multicoreParam

### Usage

    outputLibs(
      df,
      chrStyle = NULL,
      type = "default",
      envir = .GlobalEnv,
      BPPARAM = bpparam()
    )

### Arguments

`df` | an ORFik `experiment`
`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"
`type` | a character(default: "defualt"), load files in experiment or some precomputed variant, either "bedo" or "pshifted". These are made with ORFik:::simpleLibs()
`envir` | environment to save to, default (.GlobalEnv)
`BPPARAM` | how many cores? default: bpparam()

### Value

NULL (libraries set by envir assignment)

### See Also

Other ORFik_experiment: `bamVarName()`, `create.experiment()`, `experiment-class`, `libraryTypes()`, `read.experiment()`, `save.experiment()`, `validateExperiments()`

### Examples

    # 1. Pick directory
    dir <- system.file("extdata", "", package = "ORFik")
    # 2. Pick an experiment name
    exper <- "ORFik"
    # 3. Pick .gff/.gtf location
    txdb <- system.file("extdata", "annotations.gtf", package = "ORFik")
    template <- create.experiment(dir = dir, exper, txdb = txdb,
                                  viewTemplate = FALSE)
    template$X5[6] <- "heart" # <- fix non unique row
    # read experiment
    df <- read.experiment(template)
    # Output to .GlobalEnv with:
    # outputLibs(df)

[Package ORFik version 1.6.9 Index]