outputLibs {ORFik} | R Documentation |
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
outputLibs( df, chrStyle = NULL, type = "default", param = NULL, strandMode = 0, naming = "minimum", output.mode = "envir", envir = envExp(df), BPPARAM = bpparam() )
df |
an ORFik |
chrStyle |
a GRanges object, TxDb, FaFile,
or a |
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 |
By default (i.e. |
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:
|
envir |
environment to save to, default
|
BPPARAM |
how many cores/threads to use? default: bpparam().
To see number of threads used, do |
NULL (libraries set by envir assignment), unless output.mode is "list" or "envirlist": Then you get a list of the libraries.
Other ORFik_experiment:
ORFik.template.experiment()
,
bamVarName()
,
create.experiment()
,
experiment-class
,
filepath()
,
libraryTypes()
,
organism,experiment-method
,
read.experiment()
,
save.experiment()
,
validateExperiments()
## 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)