xmapBridge {exonmap} | R Documentation |
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.
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)
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. |
For more details of installation and operation, see the package vignette.
Crispin Miller
http://bioinformatics.picr.man.ac.uk/
## Not run: xmapBridge("ENSG00000000003",eset=x,gps=list(A=1:3,B=4:6),type="fc",overwrite=FALSE) ## End(Not run)