[BioC] Possible to set alternative colnames on read.flowSet (flowCore)
a.gregson at ucla.edu
Fri Mar 6 23:09:22 CET 2009
On Fri, 06 Mar 2009 13:40:23 -0800
Florian Hahne <fhahne at fhcrc.org> wrote:
> Yes there is.
> From the documentation of read.flowSet:
> name.keyword: An optional character vector that specifies which FCS
> keyword to use as the sample names. If this is not set, the
> GUID of the FCS file is used for sampleNames, and if that is
> not present (or not unique), then the file names are used.
Sorry, I'm not following you. In the examples, name.keyword is used for
the file names and appears to take a keyword from the FCS file as its
target, such as "SAMPLE ID". Maybe colname.keyword? Even then, I don't
understand how I could tell read.flowSet to read the keyword just
after the one it normally does to take the colnames. Maybe a grep
operation? The FCS keyword changes with each channel, the channel
number in the below example is augmented by one as you go along.
$`$P16N` --------------> used by read.flowSet as colnames
 "Indo-1 (Violet)-A"
$`$P16S` --------------> would like to use instead
Aric Gregson <a.gregson at ucla.edu>
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