chkMotif4TF {harbChIP} | R Documentation |
analyze relationship between motif frequency and binding intensity for selected motif and TF
chkMotif4TF(motif, TF, chset, upstr, bthresh=2, countthresh=0)
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 |
Uses countPattern
to perform
motif count.
a list with elements call
, table
,
and test
, the latter providing the result of
fisher.test
Vince Carey <stvjc@channing.harvard.edu>
# slow ## Not run: data(harbChIP) data(sceUpstr) chkMotif4TF("CGGCCG", "RDS1", harbChIP, sceUpstr) ## End(Not run)