filepath {ORFik} | R Documentation |
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.
filepath(df, type, basename = FALSE)
df |
an ORFik |
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! |
For pshifted libraries, it will load ".bedo" prioritized over ".bed", if there exists both file types for the same file.
a character vector of paths, or a list of character with 2 paths per, if paired libraries exists
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()
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")