readMapper: Retrieve a set of predicted transcription factor binding...

In RMAPPER: R interface to the MAPPER database of transcription factor binding sites

Description

The MAPPER RPC interface allows you to retrieve a set of predicted transcription factor binding sites from the MAPPER database through a simple HTTP request. This package provides a function to retrieve predicted TFBS from R.

Usage

 readMAPPER(stub = paste(urlpath, "db-rpc?", sep = ""), ...)

Arguments

stub	stub – a string giving the URL handle up to the db-rpc selector (optional)
...	... – all the query parameters (see Details).

Details

Currently (9/10) the RPC interface to MAPPER defines the following parameters. You can use any of these as keywords (with bindings supplied using "=", e.g., gene="CRP") to the readMAPPER function.

gene - you can use either NCBI GeneID or mRNA accession number; gene names should work too, but this is not recommended because there often are multiple forms of the same gene. [required, unless 'list' is specified]

models - a comma-separated list of model names (to restrict the output to these models only) [required, unless 'list' is specified]

score - the score threshold (0 by default)

perc - the percentile (one of 50, 80, 85, 90, 95). Only hits with scores above the desired percentile for each model are returned.

eval - the E-value threshold (25 by default)

pbases - how many basepairs to look at (default: 2000). See pstart.

pstart - what pbases is relative to (either T for transcript start or C for coding sequence start - remember that in the db we have hits for the region from 10,000 bp upstream of transcript start to 50bp after coding sequence start)

sort - how to sort the results: either M (by model accession), N (factor name), E (by E-value), S (by score), P (by position, the default)

org - two letter organism code

list - returns a list of all TF names with the corresponding model accession numbers. All other parameters are ignored.

If you issue rmapperHelp(), you will get a help page in text.

Value

An instance of the mapperHits class.

Author(s)

Vince Carey <[e-mail]>

References

http://genome.ufl.edu/mapper/

See Also

mapperHits-class query hits

Examples

 # Run an example retrieving data from the MAPPER RPC interface for gene ID = NM_009696
 mh = readMAPPER(gene="NM_009696", perc="95", models="M00027")
 # Display the mapperHits object returned by readMAPPER
 mh
 # Display the exact query that was issued to the MAPPER RPC interface
 query(mh)
 # Display the details of hits from the query 
 hits(mh)

RMAPPER documentation built on Sept. 12, 2016, 6:17 a.m.