matchGenes {bumphunter} | R Documentation

## Find and annotate closest genes to genomic regions

### Description

Find and annotate closest genes to genomic regions

### Usage

    matchGenes(x, subject, type = c("any", "fiveprime"), promoterDist = 2500, skipExons = FALSE, verbose = TRUE)

### Arguments

`x` | An `IRanges` or `GenomicRanges` object, or a `data.frame` with columns for `start`, `end`, and, optionally, `chr` or `seqnames`.
`subject` | An `GenomicRanges` object containing transcripts or genes that have been annotated by the function `annotateTranscripts`.
`promoterDist` | Anything within this distance to the transcription start site (TSE) will be considered a promoter.
`type` | Should the distance be computed to any part of the transcript or the five prime end.
`skipExons` | Should the annotation of exons be skipped. Skipping this part makes the code slightly faster.
`verbose` | logical value. If 'TRUE', it writes out some messages indicating progress. If 'FALSE' nothing should be printed.

### Details

This function runs `nearest` and then annotates the the relationship between the region and the transcript/gene that is closest. Many details are provided on this relationship as described in the next section.

### Value

A data frame with one row for each query and with columns `c("name", "annotation", "description", "region", "distance", "subregion", "insideDistance", "exonnumber", "nexons", "UTR", "strand", "geneL", "codingL","Entrez","subhectHits")`. The first column is the _gene_ nearest the query, by virtue of it owning the transcript determined (or chosen by `nearest`) to be nearest the query. Note that the nearest gene to a given query, in column 3, may not be unique and we arbitrarily chose one as done by default by `nearest`.

The "distance" column is the distance from the query to the 5' end of the nearest transcript, so may be different from the distance computed by `nearest` to that transcript, as a range.

`name` | Symbol of nearest gene
`annotation` | RefSeq ID
`description` | a factor with levels `c("upstream", "promoter", "overlaps 5'", "inside intron", "inside exon", "covers exon(s)", "overlaps exon upstream", "overlaps exon downstream", "overlaps two exons", "overlaps 3'", "close to 3'", "downstream", "covers")`
`region` | a factor with levels `c("upstream", "promoter", "overlaps 5'", "inside", "overlaps 3'", "close to 3'", "downstream", "covers")`
`distance` | distance before 5' end of gene
`subregion` | a factor with levels `c("inside intron", "inside exon", "covers exon(s)", "overlaps exon upstream", "overlaps exon downstream", "overlaps two exons")`
`insideDistance` | distance past 5' end of gene
`exonnumber` | which exon
`nexons` | number of exons
`UTR` | a factor with levels `c("inside transcription region", "5' UTR", "overlaps 5' UTR", "3'UTR", "overlaps 3'UTR", "covers transcription region")`
`strand` | "+" or "-"
`geneL` | the gene length
`codingL` | the coding length
`Entrez` | Entrez ID of closest gene
`subjectHits` | Index in subject of hit

### Author(s)

Harris Jaffee, Peter Murakami and Rafael A. Irizarry

### See Also

`annotateNearest`, `annotateTranscripts`

### Examples

    ## Not run:
        islands=makeGRangesFromDataFrame(read.delim("http://rafalab.jhsph.edu/CGI/model-based-cpg-islands-hg19.txt")[1:100,])
        library("TxDb.Hsapiens.UCSC.hg19.knownGene")
        genes <- annotateTranscripts(TxDb.Hsapiens.UCSC.hg19.knownGene)
        tab<- matchGenes(islands,genes)

    ## End(Not run)

[Package bumphunter version 1.28.0 Index]