chkMotif4TF {harbChIP}R Documentation

analyze relationship between motif frequency and binding intensity for selected motif and TF

Description

analyze relationship between motif frequency and binding intensity for selected motif and TF

Usage

chkMotif4TF(motif, TF, chset, upstr, bthresh=2, countthresh=0)

Arguments

motif character string in alphabet known to Biostrings
TF name of a TF (sample name in the ChIP-chip data structure chset
chset an ExpressionSet instance harboring ChIP-chip data
upstr an instance of upstreamSeqs
bthresh threshold for binding intensity results to declare TF 'bound' to the upstream region
countthresh threshold for motif count to be considered 'present' in upstream region

Details

Uses countPattern to perform motif count.

Value

a list with elements call, table, and test, the latter providing the result of fisher.test

Author(s)

Vince Carey <stvjc@channing.harvard.edu>

Examples

# slow
## Not run: 
data(harbChIP)
data(sceUpstr)
chkMotif4TF("CGGCCG", "RDS1", harbChIP, sceUpstr)
## End(Not run)

[Package harbChIP version 0.0.4 Index]