filepath: Get filepaths to ORFik experiment
In Roleren/ORFik: Open Reading Frames in Genomics

filepath

R Documentation

Get filepaths to ORFik experiment

Description

If other type than "default" is given and that type is not found (and 'fallback' is TRUE), it will return you ofst files, if they do not exist, then default filepaths without warning.

Usage

filepath(
  df,
  type,
  basename = FALSE,
  fallback = type %in% c("pshifted", "bed", "ofst", "bedoc", "bedo"),
  suffix_stem = "AUTO",
  base_folders = libFolder(df)
)

Arguments

`df`	an ORFik `experiment`
`type`	a character(default: "default"), load files in experiment or some precomputed variant, like "ofst" or "pshifted". These are made with ORFik:::convertLibs(), shiftFootprintsByExperiment(), etc. 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 must exists. Presets are (folder is relative to default lib folder, some types fall back to other formats if folder does not exist): - "default": load the original files for experiment, usually bam. - "ofst": loads ofst files from the ofst folder, relative to lib folder (falls back to default) - "pshifted": loads ofst, wig or bigwig from pshifted folder (falls back to ofst, then default) - "cov": Load covRle objects from cov_RLE folder (fail if not found) - "covl": Load covRleList objects, from cov_RLE_List folder (fail if not found) - "bed": Load bed files, from bed folder (falls back to default) - Other formats must be loaded directly with fimport
`basename`	logical, default (FALSE). Get relative paths instead of full. Only use for inspection!
`fallback`	logical, default: type If TRUE, will use type fallback, see above for info.
`suffix_stem`	character, default "AUTO". Which is "" for all except type = "pshifted". Then it is "_pshifted" appended to end of names before format. Can be vector, then it searches suffixes in priority: so if you insert c("_pshifted", ""), it will look for suffix _pshifted, then the empty suffix.
`base_folders`	character vector, default libFolder(df), path to base folder to search for library variant directories. If single path (length == 1), it will apply to all libraries in df. If df is a collection, an experiment where libraries are put in different folders and library variants like pshifted are put inside those respective folders, set base_folders = libFolder(df, mode = "all")

Details

For pshifted libraries, if "pshifted" is specified as type: if if multiple formats exist it will use a priority: ofst -> bigwig -> wig -> bed. For formats outside default, all files must be stored in the directory of the first file: base_folder <- libFolder(df)

Value

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

Examples

df <- ORFik.template.experiment()
filepath(df, "default")
# Subset
filepath(df[9,], "default")
# Other format path
filepath(df[9,], "ofst")
## If you have pshifted files, see shiftFootprintsByExperiment()
filepath(df[9,], "pshifted") # <- falls back to ofst

Roleren/ORFik documentation built on Oct. 19, 2024, 7:37 a.m.