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 1.0.0 Index]