Description Usage Arguments Value Out of memory? Slow performance? Author(s) See Also
Low-level function to read a BASE file section from a connection or a file. This a supportive function to readBaseFile().
1 2 | ## Default S3 method:
readBaseFileSection(con, suppressSingleAssayLabels=TRUE, extractSpotsData=FALSE, verbose=FALSE, ...)
|
con |
A |
suppressSingleAssayLabels |
If |
extractSpotsData |
If |
verbose |
Either a |
... |
Not used. |
Returns a named list
structure containing the parsed BASE structure.
Some BASE files are very large due to large amount of assay data in
'spots' sections. By setting argument extractSpotsData=TRUE
,
such data is written to separate files for each assay immediately after
being read and thereafter removed from memory. This means that it is
in practice possible to read BASE files with almost any number of
assays, also if they are "passed" via stdin.
The number of lines in the data table of a BASE file data section is
either not known on before hand or specified by the count
header.
If count
is available, the data table is read approximately
eight times faster than if it is not.
To the best of our knowledge, starting with BASE v1.2.17 (released
November 2005), header count
is included by default and in
previous versions it is not available at all.
If count
is not specified, the table is first read line by line
to a temporary file and then re-read by read.table()
. (The
reason for this is that read.table()
otherwise will read to end
of file, and not to the first empty line. Unfortunately, this means
that the reading of data is a bit slow.)
Henrik Bengtsson (http://www.braju.com/R/)
readBaseFile
().
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