xmapBridge              package:exonmap              R Documentation

_G_e_n_e_r_a_t_e _a _d_a_t_a _f_i_l_e _w_h_i_c_h _c_a_n _b_e _d_i_s_p_l_a_y_e_d _i_n _t_h_e _X:_M_A_P _b_r_o_w_s_e_r
_u_s_i_n_g _t_h_e _X:_M_A_P _b_r_i_d_g_e

_D_e_s_c_r_i_p_t_i_o_n:

     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.

_U_s_a_g_e:

       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)

_A_r_g_u_m_e_n_t_s:

       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.

_D_e_t_a_i_l_s:

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

_V_a_l_u_e:

_A_u_t_h_o_r(_s):

     Crispin Miller

_R_e_f_e_r_e_n_c_e_s:

     <URL:  http://bioinformatics.picr.man.ac.uk/>

_S_e_e _A_l_s_o:

_E_x_a_m_p_l_e_s:

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

