readMapper {RMAPPER}R Documentation

query and/or parse a file returned by mapper.chip.org

Description

Usage

readMapper(infile=NULL, mapperPW=NULL, 
  stub="http://mapper.chip.org/mapper/db-rpc?", models=NULL, ...)

Arguments

infile infile – pathname to a previously generated RPC output
mapperPW mapperPW – if query is supplied for CURL interchange, the credentials (in the form myname@a.b.c:mapperpw) necessary to permit the transaction
stub stub – a string giving the URL handle up to the db-rpc selector
models a vector of identifiers of MAPPER models; see their web site for codes
... ... – all the query parameters. see Details; models will default to "M1" because the XML RPC processor fails if no models parameter is set. If an unknown model parameter is set, then it seems to return all models.

Details

Currently (2/06) 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 GeneID or mRNA; gene name should work too but it's not recommended because there often are multiple forms of the same gene.

score - the score threshold (0 by default)

perc - the percentile (one of p50, p80, p85, p90, p95).

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

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

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)

models - a comma-separated list of model names (to restrict the output to these models only)

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)

Thanks to Alberto Riva for this list

Value

an instance of the mapperHits class.

Author(s)

Vince Carey <stvjc@channing.harvard.edu>

References

mapper.chip.org

Examples

readMapper(infile=system.file("txt/NM_007294.txt", package="RMAPPER"))
if (FALSE) # you must supply your credentials to succeed over the web
 readMapper(gene="NM_007294", perc="p95", mapperPW="[usern:pwd]")

[Package RMAPPER version 1.2.0 Index]