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]