outputLibs {ORFik} | R Documentation

## Output bam/bed/bedo/bedoc/ofst/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, TxDb, FaFile, 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: "default"), load files in experiment or some precomputed variant, either "bedo", "bedoc", "ofst or "pshifted". These are made with ORFik:::simpleLibs(), shiftFootprintsByExperiment()..
`envir` | environment to save to, default (.GlobalEnv)
`BPPARAM` | how many cores/threads to use? default: bpparam(). To see number of threads used, do `bpparam()$workers`

### Value

NULL (libraries set by envir assignment)

### See Also

Other ORFik_experiment: `ORFik.template.experiment()`, `bamVarName()`, `create.experiment()`, `experiment-class`, `filepath()`, `libraryTypes()`, `organism.df()`, `read.experiment()`, `save.experiment()`, `validateExperiments()`

### Examples

    ## Load a template ORFik experiment
    df <- ORFik.template.experiment()
    ## Default library type load, usually bam files
    # outputLibs(df, type = "default")
    ## .ofst file load, if ofst files does not exists
    ## it will load default
    # outputLibs(df, type = "ofst")
    ## .wig file load, if wiggle files does not exists
    ## it will load default
    # outputLibs(df, type = "wig")

[Package ORFik version 1.8.6 Index]