drawHeatMapForAtlasExperiment: Produce a heatmap of differentially expressed genes vs...

In AtlasRDF: Gene Expression Atlas query and gene set enrichment package.

Description

Draws a heatmap of genes that are differentially expressed beyond a given t stat signficance against conditions they are diff expressed for for a given Atlas experiment.

Usage

    drawHeatMapForAtlasExperiment(experimentid, tstatsignificance = 5, numoffactorsdiffexpressedacross = 1, endpoint = "http://www.ebi.ac.uk/rdf/services/atlas/sparql")

Arguments

experimentid	Atlas experiment ID which is to be visualized
tstatsignificance	The significance beyond which a gene should be included for visualisation. A significance value of '5' will only include genes with a t-stat of >= 5 or <= -5.
numoffactorsdiffexpressedacross	Draw only genes which are differentially expressed across this number of specified factors (default is 1)
endpoint	SPARQL endpoint to query data from. Default value is the live Atlas SPARQL endpoint but this can be overidden.

Value

matrix of gene names with t-statistics for level of differential expression for each factor (one factor per column)

Author(s)

Simon Jupp, James Malone

Examples

    
    #data <- drawHeatMapForAtlasExperiment("E-MTAB-1670", 12)
    

Example output

Loading required package: hash
hash-3.0.1 provided by Decision Patterns

Loading required package: SPARQL
Loading required package: XML
Loading required package: RCurl
Loading required package: bitops

AtlasRDF documentation built on Nov. 17, 2017, 9:33 a.m.