filepath {ORFik} | R Documentation

## Get filepaths to ORFik experiment

### Description

If other type than "default" is given and that type is not found, it will return you ofst files, if they do not exist, then 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. 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.
`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.zf()`, `ORFik.template.experiment()`, `bamVarName()`, `create.experiment()`, `experiment-class`, `libraryTypes()`, `organism,experiment-method`, `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")

[Package ORFik version 1.14.7 Index]