Description Usage Arguments Value Author(s) See Also Examples
Allows retrieval of the the cytoband/karyotype label for HGNC gene labels.
1 2 |
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') |
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'
Nicholas Cooper nick.cooper@cimr.cam.ac.uk
Chr
, Pos
, Pos.gene
, Band
,
Band.gene
, Band.pos
, Gene.pos
1 2 3 4 5 6 7 8 | 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)
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