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tgirke/motifEnrich.R

Last active April 11, 2021 23:58
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Motif enrichment for ChIP-Seq
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motifEnrich.R
###############################
## PWM matching in sequences ##
###############################
## Date: May 22, 2020
## Starter code for ChIP-Seq1 project
library(MotifDb)
as.list(query(MotifDb, 'athaliana'))
as.list(query(MotifDb, 'hsapiens'))
chr <- DNAStringSet(c(seq1="AAAGCTAAAGGTAAAGCAAAACGCCGCCG", seq2="CGCCGCCG"))
pwm <- as.list(query(MotifDb, 'athaliana'))[[1]]
sapply(chr, function(x) matchPWM(pwm, x, min.score="90%"))
##########################
## Matches among motifs ##
##########################
library(MotIV)
?motifMatch
egr1.motif <- MotifDb[egr1.mouse.jaspar.rows]
ts <- motifMatch(as.list (pwm), as.list (pwm), top=11)
#####################################
## Motif enrichment with PWMEnrich ##
#####################################
## see here: http://bioconductor.org/packages/release/bioc/vignettes/PWMEnrich/inst/doc/PWMEnrich.pdf
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