Once the user has a list of cytobands of interest, one downstream application could
be to find the list of genes present in the cytoband regions. This
function can be used for this purpose. The following steps should be run before this function can
#Step 1 : Run cytoband CIN - using
#Step 2: Plot cytoband level heatmap - using
#Step 3: Go through heatmaps as select one appropriate threshold. Load the file.
#Step 4: Perform T test to find differentially expressed cytobands - using
#Step 5: Call this funtion to extract genes located in cytoband regions
#More details and tutorial are given in the accompanying vignette
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Output of the cytoband T test results
Information about CDS start and end positions, Gene names
Name of output folder
Output files: The genes names present in the cytoband regions
See accompanying vignette for an end-to-end tutorial
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#For this example, we load example T test output object data("cyto.cin4heatmap") data("hg18.ucsctrack") #load Hg 18 reference annotation file data("geneAnno") #load Gene annotations file extract.genes.in.cyto.regions(cyto.cin4heatmapObj =cyto.cin4heatmap, genome.ucsc = hg18.ucsctrack, gene.annotations = geneAnno)
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