xmapBridge {exonmap}R Documentation

Generate a data file which can be displayed in the X:MAP browser using the X:MAP bridge

Description

Writes out a datafile containing expression data for the gene of interest. This file is stored in a cache directory specified by the environment R\_XMAP\_BRIDGE\_CACHE. When the xmapBridge is running locally, the file will be detected, and can be displayed in the X:MAP genome browser.

Note that in order to use this function, the line species=homo_sapiens (or mus_musculus or rattus_norvegicus) must be specified as an additional line in the .mycnf file for the appropriate database. See the exonmap installation instructions for more details.

Usage

  xmapBridge(x,eset,colours,bridge.file=getBridgeFile(x),description="exonmap expression data",gps,type=c("fc","int"),overwrite=FALSE,show.introns=TRUE,show.mt=FALSE,open.browser=FALSE,ylim)
  getBridgeFile(basename)

Arguments

x Ensembl gene identifier for the gene to plot
eset ExpressionSet object containing expression data to plot
colours Can be used to specify explicitly what colours to plot the expression data in the browser. If specified, must be a character vector of hexadecimal strings (e.g. #0000FF) the same length as there are groups in the parameter 'gps'.
bridge.file Where should the output file be written. By default, the filename is generated by getBridgeFile.
description free text description of this expression dataset - is shown in the browser
gps A list of vectors providing indices into the expression data to specify how samples should be grouped together. If fold change data are plotted, then there must be exactly two groups. For example gps=list(cellLineA=1:3,cellLineB=4:6) would specify two groups, called cellLineA and cellLineB, each consisting of three samples (1,2,3 and 4,5,6).
type The type of plot to draw. fc specifies fold change, int, intensity.
overwrite Unless TRUE the function will not overwrite an existing data file
show.introns If FALSE, plot only exon data.
show.mt If TRUE, show data for multi-target probesets
open.browser If TRUE, attempt to open the default web browser showing X:MAP centered on the specified gene.
ylim Can be used to specify the Y bounds of the plot. By default they are c(0,14) for intensity, c(-5,5) for fold change. Data that exceed these limits are truncated to the maximum or minimum values.
basename base filename from which to construct the full path to an xmap bridge file in the cache directory.

Details

For more details of installation and operation, see the package vignette.

Author(s)

Crispin Miller

References

http://bioinformatics.picr.man.ac.uk/

Examples

 
  ## Not run: 
    xmapBridge("ENSG00000000003",eset=x,gps=list(A=1:3,B=4:6),type="fc",overwrite=FALSE)
  
## End(Not run)

[Package exonmap version 1.6.06 Index]