readQseq {ShortRead} | R Documentation |
readQseq
reads all files matching pattern
in a directory
into a single ShortReadQ
-class object.
Information on machine, lane, tile, x, and y coordinates, filtering
status, and read number are not returned (although filtering status
can be used to selectively include reads as descrbied below).
readQseq(dirPath, pattern = character(0), ..., as=c("ShortReadQ", "XDataFrame"), filtered=FALSE, verbose=FALSE)
dirPath |
Directory path or other object (e.g.,
SolexaPath ) for which methods are defined. |
pattern |
Regular expression matching names of _qseq files
to be summarized. |
... |
Additional argument, passed to I/O functions. |
as |
character(1) indicating the class of the return
type. |
filtered |
logical(1) indicating whether to include only
those reads passing Solexa filtering? |
verbose |
logical(1) indicating whether to report on
progress during evaluation. |
An object of class ShortReadQ
.
Martin Morgan <mtmorgan@fhcrc.org>
fl <- system.file("extdata", package="ShortRead") sp <- SolexaPath(fl) readQseq(sp)