outputLibs: Output bam/bed/bedo/bedoc/ofst/wig files to R as variables

In ORFik: Open Reading Frames in Genomics

Description

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

Usage

outputLibs(
  df,
  chrStyle = NULL,
  type = "default",
  param = NULL,
  strandMode = 0,
  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 "ofst", "bedo", "bedoc" or "pshifted". These are made with ORFik:::convertLibs() or shiftFootprintsByExperiment(). Can also be custom user made folders inside the experiments bam folder.
param	NULL or a ScanBamParam object. Like for scanBam, this influences what fields and which records are imported. However, note that the fields specified thru this ScanBamParam object will be loaded in addition to any field required for generating the returned object (GAlignments, GAlignmentPairs, or GappedReads object), but only the fields requested by the user will actually be kept as metadata columns of the object. By default (i.e. param=NULL or param=ScanBamParam()), no additional field is loaded. The flag used is scanBamFlag(isUnmappedQuery=FALSE) for readGAlignments, readGAlignmentsList, and readGappedReads. (i.e. only records corresponding to mapped reads are loaded), and scanBamFlag(isUnmappedQuery=FALSE, isPaired=TRUE, hasUnmappedMate=FALSE) for readGAlignmentPairs (i.e. only records corresponding to paired-end reads with both ends mapped are loaded).
strandMode	numeric, default 0. Only used for paired end bam files. One of (0: strand = *, 1: first read of pair is +, 2: first read of pair is -). See ?strandMode. Note: Sets default to 0 instead of 1, as readGAlignmentPairs uses 1. This is to guarantee hits, but will also make mismatches of overlapping transcripts in opposite directions.
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")

ORFik documentation built on March 27, 2021, 6 p.m.