grepEcols: Returns the matching column names of indices.

In lgatto/MSnbase: Base Functions and Classes for Mass Spectrometry and Proteomics

Returns the matching column names of indices.

Description

Given a text spread sheet f and a pattern to be matched to its header (first line in the file), the function returns the matching columns names or indices of the corresponding data.frame.

The function starts by reading the first line of the file (or connection) f with readLines, then splits it according to the optional ... arguments (it is important to correctly specify strsplit's split character vector here) and then matches pattern to the individual column names using grep.

Similarly, getEcols can be used to explore the column names and decide for the appropriate pattern value.

These functions are useful to check the parameters to be provided to readMSnSet2.

Usage

grepEcols(f, pattern, ..., n = 1)

getEcols(f, ..., n = 1)

Arguments

f	A connection object or a character string to be read in with readLines(f, n = 1).
pattern	A character string containing a regular expression to be matched to the file's header.
...	Additional parameters passed to strsplit to split the file header into individual column names.
n	An integer specifying which line in file f to grep (get). Default is 1. Note that this argument must be named.

Value

Depending on value, the matching column names of indices. In case of getEcols, a character of column names.

Author(s)

Laurent Gatto

See Also

readMSnSet2

lgatto/MSnbase documentation built on Nov. 12, 2024, 10:58 a.m.