[BioC] ChIPpeakAnno "examplePattern.fa" file

[Paul Shannon]

I offer below a short example of using rGADEM with MotifDb which you may find useful.  

The example motivates and then demonstrates "seeded" search, in which a candidate TF is provided to rGADEM.  (The rGADEM vignette illustrates the simpler task of de novo motif search.

 - Paul


On Feb 27, 2013, at 9:03 AM, Zhu, Lihua (Julie) wrote:

> Jose,
> 
> Thanks for your kind word!
> 
> You might want to check out rGADEM package for de nova motif discovery.
> 
> Best regards,
> 
> Julie
> 

library(rGADEM)
library(MotifDb)
library(BSgenome.Hsapiens.UCSC.hg19)
path <- system.file("extdata/Test_100.fasta", package="rGADEM")
sequences <- readDNAStringSet(path, "fasta")
length(sequences)   # 49

   # you can use the UCSC genome browser to BLAT the first 4 sequences, one at a time,
   # against human hg19, and see what TFs bind there
   #   http://genome.ucsc.edu/cgi-bin/hgBlat?command=start

as.character(substr(sequences[1:4], 1, 80))

   # Once you blat, click through to view the blat match in the genome browser,
   # and enable the "Transcription Factor ChIP-seq from ENCODE" track.
   # The FOXA1 Tf has a high score in this region of chr1
   # for most of these sequences

   # obtain the reported motif for this TF from the Bioc MotifDb package

query(MotifDb, 'foxa1')

   # MotifDb object of length 1
   # | Created from downloaded public sources: 2012-Nov-01
   # | 1 position frequency matrices from 1 source:
   # |        JASPAR_CORE:    1
   # | 1 organism/s
   # |           Hsapiens:    1
   # Hsapiens-JASPAR_CORE-FOXA1-MA0148.1 

   # now use rGADEM to do a seeded search:

pwm.foxa1 <- as.list(MotifDb["Hsapiens-JASPAR_CORE-FOXA1-MA0148.1"])
gadem.foxa1 <-GADEM(sequences,verbose=1,genome=Hsapiens,Spwm=pwm.foxa1, seed=TRUE)
consensus(gadem.foxa1)

   # [1] "nTGTTTACwyw"      "GmwGrrrsswGGvAGn"

   # how do the 49 sequences match to these two motifs?
mean(sapply(gadem.foxa1 at motifList[[1]]@alignList, function(x) x at pval))
mean(sapply(gadem.foxa1 at motifList[[2]]@alignList, function(x) x at pval))


On Feb 27, 2013, at 9:03 AM, Zhu, Lihua (Julie) wrote:

> Jose,
> 
> Thanks for your kind word!
> 
> You might want to check out rGADEM package for de nova motif discovery.
> 
> Best regards,
> 
> Julie
>