readXStringColumns {ShortRead} | R Documentation

## Read one or more columns into XStringSet (e.g., DNAStringSet) objects

### Description

This function allows short read data components such as DNA sequence, quality scores, and read names to be read in to `XStringSet` (e.g., `DNAStringSet`, `BStringSet`) objects. One or several files of identical layout can be specified.

### Usage

    readXStringColumns(dirPath, pattern=character(0),
                       colClasses=list(NULL),
                       nrows=-1L, skip=0L,
                       sep = "\t", header = FALSE, comment.char="#")

### Arguments

`dirPath` | A character vector giving the directory path (relative or absolute) of files to be read.
`pattern` | The (`grep`-style) pattern describing file names to be read. The default (`character(0)`) reads all files in `dirPath`. All files are expected to have identical numbers of columns.
`colClasses` | A list of length equal to the number of columns in a file. Columns with corresponding `colClasses` equal to `NULL` are ignored. Other entries in `colClasses` are expected to be character strings describing the base class for the `XStringSet`. For instance a column of DNA sequences would be specified as `"DNAString"`. The column would be parsed into a `DNAStringSet` object.
`nrows` | A length 1 integer vector describing the maximum number of `XString` objects to read into the set. Reads may come from more than one file when `dirPath` and `pattern` parse several files and `nrow` is greater than the number of reads in the first file.
`skip` | A length 1 integer vector describing how many lines to skip at the start of each file.
`sep` | A length 1 character vector describing the column separator.
`header` | A length 1 logical vector indicating whether files include a header line identifying columns. If present, the header of the first file is used to name the returned values.
`comment.char` | A length 1 character vector, with a single character that, when appearing at the start of a line, indicates that the entire line should be ignored. Currently there is no way to use comment characters in other than the first position of a line.

### Value

A list, with each element containing an `XStringSet` object of the type corresponding to the non-NULL elements of `colClasses`.

### Author(s)

Martin Morgan <mtmorgan@fhcrc.org>

### Examples

    ## valid character strings for colClasses
    names(slot(getClass("XString"), "subclasses"))

    dirPath <- system.file('extdata', 'maq', package='ShortRead')

    colClasses <- rep(list(NULL), 16)
    colClasses[c(1, 15, 16)] <- c("BString", "DNAString", "BString")

    ## read one file
    readXStringColumns(dirPath, "out.aln.1.txt", colClasses=colClasses)

    ## read all files into a single object for each column
    res <- readXStringColumns(dirPath, colClasses=colClasses)

[Package ShortRead version 1.45.4 Index]