ShortRead: countLines – R documentation

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countLines

Count lines in all (text) files in a directory whose file name matches a pattern

Description

countLines visits all files in a directory path dirPath whose base (i.e., file) name matches pattern. Lines in the file are counted as the number of new line characters.

Usage

countLines(dirPath, pattern=character(0), ..., useFullName=FALSE)

Arguments

`dirPath`	A character vector (or other object; see methods defined on this generic) giving the directory path (relative or absolute) of files whose lines are to be counted.
`pattern`	The (`grep`-style) pattern describing files whose lines are to be counted. The default (`character(0)`) results in line counts for all files in the directory.
`...`	Additional arguments, passed internally to list.files. See `list.files`.
`useFullName`	A `logical(1)` indicating whether elements of the returned vector should be named with the base (file) name (default; `useFullName=FALSE`) or the full path name (`useFullName=TRUE`).

Value

A named integer vector of line counts. Names are paths to the files whose lines have been counted, excluding dirPath.

Author(s)

Martin Morgan

Examples

sp <- SolexaPath(system.file('extdata', package='ShortRead'))
countLines(analysisPath(sp))
countLines(experimentPath(sp), recursive=TRUE)
countLines(experimentPath(sp), recursive=TRUE, useFullName=TRUE)

ShortRead

FASTQ input and manipulation

v1.48.0

Artistic-2.0

Authors

Martin Morgan, Michael Lawrence, Simon Anders

Initial release