grepEcols: Returns the matching column names of indices.
In MSnbase: Base Functions and Classes for Mass Spectrometry and Proteomics

Description Usage Arguments Details Value Author(s) See Also

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.

1
2
3

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

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

`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.

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.

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

Laurent Gatto

readMSnSet2

MSnbase documentation built on Jan. 23, 2021, 2 a.m.