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, 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: "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 1.7.21 Index]