dot-getPairedFromFilename: Constructor for paired-end experiments

In GiBacci/expR:

Constructor for paired-end experiments

Description

This funciton is similar to getSingleEndFromFilename but it can parse forward and reverse files separately.

Usage

.getPairedFromFilename(maindir = ".", forward = "_R1_",
  reverse = "_R2_", samples = NULL, run = NULL, output = NULL,
  recursive = F)

Arguments

maindir	character. The directory in which to search for sequence files.
forward	regular expression. Only file names which match the regular expression will be returned as forward files.
reverse	regular expression. Only file names which match the regular expression will be returned as reverse files.
samples	it can be NULL, a character vector, or a funciton. If it's NULL then file names will be used as sample names. If it's a character vector sample will be called using the names provided. If it's a function file names will be processed using the function provided and samples will have the resulting names.
run	one of "none", "folder", or "header". If "none" no run will be specified, if "folder" the run id will be inferred from the folder structure, and if "header" the run id will be parsed from the header of the sequences.
output	similar to samples parameter
recursive	logical. Should the listing recurse into directories?

Value

a paired-end experiment

See Also

formatSample(), formatOutptut(), and runFromHeader() for sample, output, and run formatting.

GiBacci/expR documentation built on Oct. 15, 2022, 12:15 a.m.