filepath: Get filepaths to ORFik experiment

In ORFik: Open Reading Frames in Genomics

Description

If other type than "default" is given and that type is not found, it will return you default filepaths without warning.

Usage

filepath(df, type, basename = FALSE)

Arguments

df	an ORFik experiment
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.
basename	logical, default (FALSE). Get relative paths instead of full. Only use for inspection!

Details

For pshifted libraries, it will load ".bedo" prioritized over ".bed", if there exists both file types for the same file.

Value

a character vector of paths, or a list of character with 2 paths per, if paired libraries exists

See Also

Other ORFik_experiment: ORFik.template.experiment(), bamVarName(), create.experiment(), experiment-class, libraryTypes(), organism.df(), outputLibs(), read.experiment(), save.experiment(), validateExperiments()

Examples

df <- ORFik.template.experiment()
filepath(df, "default")
# If you have bedo files, see simpleLibs():
# filepath(df, "bedo")
# If you have pshifted files, see shiftFootprintsByExperiment():
# filepath(df, "pshifted")

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