outputLibs {ORFik}R Documentation

Output NGS libraries to R as variables

Description

By default loads the original files of the experiment into the global environment, named by the rows of the experiment required to make all libraries have unique names.
Uses multiple cores to load, defined by multicoreParam

Usage

outputLibs(
  df,
  chrStyle = NULL,
  type = "default",
  param = NULL,
  strandMode = 0,
  naming = "minimum",
  output.mode = "envir",
  envir = envExp(df),
  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. It acts in a recursive manner with priority: If you state "pshifted", but it does not exist, it checks "ofst". If no .ofst files, it uses "default", which always exists.

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.

naming

a character (default: "minimum"). Name files as minimum information needed to make all files unique. Set to "full" to get full names.

output.mode

character, default "envir". Output libraries to environment. Alternative: "list", return as list. "envirlist", output to envir and return as list. If output is list format, the list elements are named from: bamVarName(df.rfp) (Full or minimum naming based on 'naming' argument)

envir

environment to save to, default envExp(df), which defaults to .GlobalEnv

BPPARAM

how many cores/threads to use? default: bpparam(). To see number of threads used, do bpparam()$workers. You can also add a time remaining bar, for a more detailed pipeline.

Value

NULL (libraries set by envir assignment), unless output.mode is "list" or "envirlist": Then you get a list of the libraries.

See Also

Other ORFik_experiment: ORFik.template.experiment(), bamVarName(), create.experiment(), experiment-class, filepath(), libraryTypes(), organism,experiment-method, 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")
## Load as list
outputLibs(df, output.mode = "list")
## Load libs to new environment (called ORFik in Global)
# outputLibs(df, envir = assign(df@experiment, new.env(parent = .GlobalEnv)))
## Load to hidden environment given by experiment
# envExp(df) <- new.env()
# outputLibs(df)


[Package ORFik version 1.12.13 Index]