Create annotation features

Generate annotation features (feature.gr for view3dStructure) from TxDb and Org object.

getFeatureGR(
  txdb,
  org,
  range,
  keytype = "ENTREZID",
  geneSymbolColumn = "SYMBOL",
  cols = seq.int(7)
)

Arguments

txdb

An TxDb object.

org

An OrgDb object.

range

GRanges object. The coordinates.

geneSymbolColumn, keytype

The column names in the OrgDb for key of TxDb and the gene symnbols.

cols

The colors for each gene.

Value

A GRanges object

Examples

library(TxDb.Hsapiens.UCSC.hg38.knownGene)
#> Loading required package: GenomicFeatures
#> Loading required package: BiocGenerics
#> Loading required package: generics
#> 
#> Attaching package: 'generics'
#> The following objects are masked from 'package:base':
#> 
#>     as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
#>     setequal, union
#> 
#> Attaching package: 'BiocGenerics'
#> 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, aperm, append,
#>     as.data.frame, basename, cbind, colnames, dirname, do.call,
#>     duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
#>     mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
#>     rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
#>     unsplit, which.max, which.min
#> Loading required package: S4Vectors
#> Loading required package: stats4
#> 
#> Attaching package: 'S4Vectors'
#> The following object is masked from 'package:utils':
#> 
#>     findMatches
#> The following objects are masked from 'package:base':
#> 
#>     I, expand.grid, unname
#> Loading required package: IRanges
#> Loading required package: Seqinfo
#> Loading required package: GenomicRanges
#> Loading required package: AnnotationDbi
#> Loading required package: Biobase
#> Welcome to Bioconductor
#> 
#>     Vignettes contain introductory material; view with
#>     'browseVignettes()'. To cite Bioconductor, see
#>     'citation("Biobase")', and for packages 'citation("pkgname")'.
library(org.Hs.eg.db)
#> 
library(GenomicRanges)
range <- GRanges("chr21:28000001-29200000")
feature.gr <- getFeatureGR(txdb = TxDb.Hsapiens.UCSC.hg38.knownGene,
                org = org.Hs.eg.db,
                range = range)
#>   2169 genes were dropped because they have exons located on both strands of
#>   the same reference sequence or on more than one reference sequence, so cannot
#>   be represented by a single genomic range.
#>   Use 'single.strand.genes.only=FALSE' to get all the genes in a GRangesList
#>   object, or use suppressMessages() to suppress this message.
#> 'select()' returned 1:1 mapping between keys and columns