extract.genes.in.cyto.regions: Given an input of cytobands, it outputs a list of genes that...
In CINdex: Chromosome Instability Index

Description Usage Arguments Value See Also Examples

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

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

`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

Output files: The genes names present in the cytoband regions

See accompanying vignette for an end-to-end tutorial

#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)

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges
Loading required package: GenomeInfoDb