read.columns {limma} | R Documentation

## Read specified columns from a file

### Description

Reads specified columns from a file in table format and creates a data frame from it, with cases corresponding to lines and variables to fields in the file.

### Usage

    read.columns(file, required.col=NULL, text.to.search="", sep="\t", quote="\"", skip=0,
                 fill=TRUE, blank.lines.skip=TRUE, comment.char="", allowEscapes=FALSE, ...)

### Arguments

`file` | the name of the file which the data are to be read from.
`required.col` | character vector of names of the required columns
`text.to.search` | character string. If any column names can be found in this string, those columns will also be read.
`sep` | the field separator character
`quote` | character string of characters to be treated as quote marks
`skip` | the number of lines of the data file to skip before beginning to read data.
`fill` | logical: if `TRUE` then in case the rows have unequal length, blank fields are implicitly added.
`blank.lines.skip` | logical: if `TRUE` blank lines in the input are ignored.
`comment.char` | character: a character vector of length one containing a single character or an empty string.
`allowEscapes` | logical. Should C-style escapes such as \n be processed or read verbatim (the default)?
`...` | other arguments are passed to `read.table`, excluding the following which are reserved and cannot be set by the user: `header`, `col.names`, `check.names` and `colClasses`.

### Details

This function is an interface to `read.table` in the base package. It uses `required.col` and `text.to.search` to set up the `colClasses` argument of `read.table`.

Note the following arguments of `read.table` are used by `read.columns` and therefore cannot be set by the user: `header`, `col.names`, `check.names` and `colClasses`.

This function is used by `read.maimages`.

### Value

A data frame (data.frame) containing a representation of the data in the file.

### Author(s)

Gordon Smyth

### See Also

`read.maimages`, `read.table`.

An overview of LIMMA functions for reading data is given in 03.ReadingData.

[Package limma version 3.42.2 Index]