CINdex (version 1.0.2)

extract.genes.in.cyto.regions: Given an input of cytobands, it outputs a list of genes that are present in the cytoband regions

Description

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 extract.genes.in.cyto.regions function can be used for this purpose. The following steps should be run before this function can be called: #Step 1 : Run cytoband CIN - using run.cin.chr() #Step 2: Plot cytoband level heatmap - using comp.heatmap() #Step 3: Go through heatmaps as select one appropriate threshold. Load the file. #Step 4: Perform T test to find differentially expressed cytobands - using ttest.cyto.cin.heatmap() #Step 5: Call this funtion to extract genes located in cytoband regions #More details and tutorial are given in the accompanying vignette

Usage

extract.genes.in.cyto.regions(cyto.cin4heatmapObj = NULL, genome.ucsc = NULL, gene.annotations = NULL, folder.name = "output_genename")

Arguments

cyto.cin4heatmapObj

Output of the cytoband T test results

genome.ucsc

Reference sequence

gene.annotations

Information about CDS start and end positions, Gene names

folder.name

Name of output folder

Value

Output files: The genes names present in the cytoband regions

See Also

See accompanying vignette for an end-to-end tutorial

Examples

#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)