Hi List
I have data in the following form:
Gene TFBS
NUDC PPARA(1) HNF4(20) HNF4(96) AHRARNT(104) CACBINDINGPROTEIN(149)
T3R(167) HLF(191)
RPA2 STAT4(57) HEB(251)
TAF12 PAX3(53) YY1(92) BRCA(99) GLI(101)
EIF3I NERF(10) P300(10)
TRAPPC3 HIC1(3) PAX5(17) PAX5(110) NRF1(119) HIC1(122)
TRAPPC3 EGR(26) ZNF219(27) SP3(32) EGR(32) NFKAPPAB65(89) NFKAPPAB(89)
RFX(121) ZTA(168)
NDUFS5 WHN(14) ATF(57) EGR3(59) PAX5(99) SF1(108) NRSE(146)
TIE1 NRSE(129)
I would like to test the 2nd column (each value has letters followed by numbers
in brackets) here for enrichment via fisher.test.
To that end I am trying to create two factors made up of column 1 (Gene) and
column 2 (TFBS) where each Gene would have several entries matching each TFBS.
My main problem just now is that I can't split the TFBS column into separate
strings (at the moment that 2nd column is all one string for each Gene).
Here's where I am just now:
test<-as.character(dataIn[,2]) # convert the 2nd column from factor to character
test2<-unlist(strsplit(test[1], ' ')) # split the first element into individual
strings (only the first element just now because I'm joust trying to get things
working)
test3<-unlist(strsplit(test2, '\\([0-9]\\)')) # get rid of numbers and brackets
now this does not behave as I hoped - it gives me:
> test3
[1] "PPARA" "HNF4(20)" "HNF4(96)"
[4] "AHRARNT(104)" "CACBINDINGPROTEIN(149)" "T3R(167)"
[7] "HLF(191)"
ie it only removes the numbers and brackets from the first entry and not the
others.
Could someone point out my mistake please?
Once I have all the TFBS (letters only) for each Gene I would then count how
often a TFBS occurs and use this data for a fisher.test testing for enrichment
of TFBS in the list I have. I'm a rather muddled here though and would
appreciate advice on whether this is the right approach.
Thanks
Iain
> sessionInfo()
R version 2.9.0 (2009-04-17)
x86_64-pc-linux-gnu
locale:
LC_CTYPE=en_GB.UTF-8;LC_NUMERIC=C;LC_TIME=en_GB.UTF-8;LC_COLLATE=en_GB.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_GB.UTF-8;LC_PAPER=en_GB.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_GB.UTF-8;LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
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