[BioC] Possible to set alternative colnames on read.flowSet (flowCore)

[Aric Gregson]

Florian,

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. 

$`$P13N`
[1] "AmCyan-A"

$`$P13S`
"AmCyan-CD3"
.
.
.
$`$P16N`   --------------> used by read.flowSet as colnames
 [1] "Indo-1 (Violet)-A"

$`$P16S`   --------------> would like to use instead
[1] "BlueUV-Live"

Thanks,

Aric
-- 
Aric Gregson <a.gregson at ucla.edu>