extract.genes.in.cyto.regions {CINdex} | R Documentation

## 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)

[Package CINdex version 1.16.0 Index]