dot-getSingleEndFromFilename: Constructor for single-end experiments

In GiBacci/expR:

Constructor for single-end experiments

Description

This function will return a single end experiment based on the name of the files selected.

Usage

.getSingleEndFromFilename(maindir = ".", pattern = ".fastq",
  samples = NULL, run = NULL, output = NULL, recursive = F)

Arguments

maindir	character. The directory in which to search for sequence files.
pattern	regular expression. Only file names which match the regular expression will be returned.
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	it can be NULL, a character vector, or a funciton. If it's NULL then no run will be assigned. If it's a character vector run 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.
output	similar to samples parameter
recursive	logical. Should the listing recurse into directories?

Value

a Single-end experiment

See Also

formatSample() and formatOutptut() for sample and output formatting.

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