reading CLAN output (.cex files) into R

rose maier rosie.maier at
Wed Jun 5 06:42:41 UTC 2013

I am running CHIP on several transcripts, and I would like to import the 
output statistics into another program (R) for analysis. In particular, I 
want to be able to read in the ADU, CHI, ASR, and CSR stats (the +d1 
portion of the output). R doesn't seem able to read the .cex files (I am 
using the R function read.table, if you happen to be familiar with that), 
so I was hoping to switch the CLAN output format to something like .txt 
instead. In the manual, the section on the +f switch seems to suggest that 
it is possible to change the file extension by typing +f.txt, but when I do 
this, I just get files that end with ".txt.cex". I've tried it with and 
without quotes around the .txt in the +f switch, and with several commands 
other than CHIP, such as FREQ and KWAL. I continue to get .txt.cex files in 
my output folder no matter what I do. 
This is the command I'm using in CLAN:
chip +bMOT +cCHI +g +harticles.cut +hsubpro.cut +hpronounobjs.cut 
-hexclude.cut +d1 +f.txt *.cha
I'm running it on a MacBook Pro (OSX 10.6.8) and I'm pretty sure I'm using 
the most recent version of CLAN (I re-installed it about a week ago). 
Any assistance you can provide would be much appreciated. Or perhaps there 
is a totally different, more straight forward way to export CLAN output 
into data tables or spreadsheets? 
Thanks in advance,
Rose Maier

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