hwgcodCHRLOC is an R object that maps manufacturer identifiers to the
starting position of the gene. The position of a gene is
measured as the number of base pairs.
The CHRLOCEND mapping is the same as the CHRLOC mapping except that it
specifies the ending base of a gene instead of the start.
Details
Each manufacturer identifier maps to a named vector of chromosomal locations,
where the name indicates the chromosome. Due to inconsistencies that
may exist at the time the object was built, these vectors may
contain more than one chromosome and/or location. If the chromosomal
location is unknown, the vector will contain an NA.
Chromosomal locations on both the sense and antisense strands are
measured as the number of base pairs from the p (5' end of the sense
strand) to q (3' end of the sense strand) arms. Chromosomal locations on the
antisense strand have a leading "-" sign (e. g. -1234567).
Since some genes have multiple start sites, this field can map to
multiple locations.
Mappings were based on data provided by: UCSC Genome Bioinformatics (Homo sapiens)
ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19
With a date stamp from the source of: 2010-Mar22
Examples
x <- hwgcodCHRLOC
# Get the probe identifiers that are mapped to chromosome locations
mapped_probes <- mappedkeys(x)
# Convert to a list
xx <- as.list(x[mapped_probes])
if(length(xx) > 0) {
# Get the CHRLOC for the first five probes
xx[1:5]
# Get the first one
xx[[1]]
}
Results
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(hwgcod.db)
Loading required package: AnnotationDbi
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, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, 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, rownames, sapply, setdiff, sort, table, tapply, union,
unique, unsplit
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")'.
Loading required package: IRanges
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
colMeans, colSums, expand.grid, rowMeans, rowSums
Loading required package: org.Hs.eg.db
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/hwgcod.db/hwgcodCHRLOC.Rd_%03d_medium.png", width=480, height=480)
> ### Name: hwgcodCHRLOC
> ### Title: Map Manufacturer IDs to Chromosomal Location
> ### Aliases: hwgcodCHRLOC hwgcodCHRLOCEND
> ### Keywords: datasets
>
> ### ** Examples
>
> x <- hwgcodCHRLOC
> # Get the probe identifiers that are mapped to chromosome locations
> mapped_probes <- mappedkeys(x)
> # Convert to a list
> xx <- as.list(x[mapped_probes])
> if(length(xx) > 0) {
+ # Get the CHRLOC for the first five probes
+ xx[1:5]
+ # Get the first one
+ xx[[1]]
+ }
21
45432205
>
>
>
>
>
> dev.off()
null device
1
>