humarray (version 1.0.0)

Band.gene: Retrieve the cytoband(s) for genes labels

Description

Allows retrieval of the the cytoband/karyotype label for HGNC gene labels.

Usage

Band.gene(genes, build = NULL, dir = getwd(), append.chr = TRUE, data.frame = FALSE, warnings = TRUE)

Arguments

genes

character, an optional vector of gene ids, or RangedData/GRanges object

build

character, "hg18" or "hg19" (or 36/37) to show which reference to retrieve. The default when build is NULL is to use the build from the current ChipInfo annotation

dir

character, 'dir' is the location to download cyto annotation information; if left as NULL, depending on the value of getOption("save.annot.in.current"), the annotation will either be saved in the working directory to speed-up subsequent lookups, or deleted after use.

append.chr

logical, it is typical that the chromosome character preceeds cytoband labels, but if this parameter is set to FALSE, it will be left off.

data.frame

logical, if data.frame is true, instead of returning a vector of full cytoband labels, a data.frame will be returned.

warnings

logical, if warnings=FALSE and SNP ids are entered instead of Gene labels, then the function will automatically detect this and return the result of Band(snps='genes')

Value

Returns a vector of bands, if any entries span more than one band, the bands will be concatenated as character type, delimited by semicolons (;). If data.frame is true, instead of returning a vector of full cytoband labels, a data.frame will be returned with a 'chr' [chromosome] column, 'band' cytoband label without the chromosome prefix, and rownames equal to 'genes'

See Also

Chr, Pos, Pos.gene, Band, Band.gene, Band.pos, Gene.pos

Examples

setwd(tempdir())
a.few.snps <- c("rs3842724","imm_11_2147527","rs9467354")
Band.gene("HLA-C") # using chr,pos vectors
Band.gene(a.few.snps)  # fails with warning as these are SNPs, not genes
Band.gene(a.few.snps,warnings=FALSE) # with warnings=FALSE this continues with snps entered
Band.gene("SLC6A4")  # serotonin gene [5-HTT]
Band.gene("SLC6A4",append.chr=FALSE)
Band.gene("SLC6A4",data.frame=TRUE)