readXStringColumns {ShortRead} | R Documentation |
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.
readXStringColumns(dirPath, pattern=character(0), colClasses=list(NULL), sep = "\t", header = FALSE, comment.char="#")
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. |
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. |
A list, with each element containing an XStringSet
object of
the type corresponding to the non-NULL elements of colClasses
.
Martin Morgan <mtmorgan@fhcrc.org>
## 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)