outputLibs {ORFik} | R Documentation |
Variable names defined by df (ORFik experiment DataFrame) Uses multiple cores to load, defined by multicoreParam
outputLibs( df, chrStyle = NULL, type = "default", param = NULL, strandMode = 0, envir = .GlobalEnv, 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. |
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. |
envir |
environment to save to, default (.GlobalEnv) |
BPPARAM |
how many cores/threads to use? default: bpparam().
To see number of threads used, do |
NULL (libraries set by envir assignment)
Other ORFik_experiment:
ORFik.template.experiment()
,
bamVarName()
,
create.experiment()
,
experiment-class
,
filepath()
,
libraryTypes()
,
organism.df()
,
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")