R: Maps between Manufacturer Identifiers and PubMed Identifiers
illuminaMousev1p1PMID
R Documentation
Maps between Manufacturer Identifiers and PubMed Identifiers
Description
illuminaMousev1p1PMID is an R object that provides mappings between
manufacturer identifiers and PubMed identifiers.
illuminaMousev1p1PMID2PROBE is an R object that provides mappings between
PubMed identifiers and manufacturer identifiers.
Details
When illuminaMousev1p1PMID is viewed as a list each manufacturer
identifier is mapped to a named vector of PubMed identifiers. The name
associated with each vector corresponds to the manufacturer
identifier. The length of the vector may be one or greater, depending
on how many PubMed identifiers a given manufacturer identifier is
mapped to. An NA is reported for any manufacturer identifier
that cannot be mapped to a PubMed identifier.
When illuminaMousev1p1PMID2PROBE is viewed as a list each PubMed
identifier is mapped to a named vector of manufacturer
identifiers. The name represents the PubMed identifier and the vector
contains all manufacturer identifiers that are represented by that
PubMed identifier. The length of the vector may be one or longer,
depending on how many manufacturer identifiers are mapped to a given
PubMed identifier.
Titles, abstracts, and possibly full texts of articles can be obtained
from PubMed by providing a valid PubMed identifier. The pubmed function of
annotate can also be used for the same purpose.
Mappings were based on data provided by: Entrez Gene
ftp://ftp.ncbi.nlm.nih.gov/gene/DATA
With a date stamp from the source of: 2015-Mar17
x <- illuminaMousev1p1PMID
# Get the probe identifiers that are mapped to any PubMed ID
mapped_probes <- mappedkeys(x)
# Convert to a list
xx <- as.list(x[mapped_probes])
if(length(xx) > 0){
# Get the PubMed identifiers for the first two probe identifiers
xx[1:2]
# Get the first one
xx[[1]]
if(interactive() && !is.null(xx[[1]]) && !is.na(xx[[1]])
&& require(annotate)){
# Get article information as XML files
xmls <- pubmed(xx[[1]], disp = "data")
# View article information using a browser
pubmed(xx[[1]], disp = "browser")
}
}
# Now convert the reverse map object illuminaMousev1p1PMID2PROBE to a list
xx <- as.list(illuminaMousev1p1PMID2PROBE)
if(length(xx) > 0){
# Get the probe identifiers for the first two PubMed identifiers
xx[1:2]
# Get the first one
xx[[1]]
if(interactive() && require(annotate)){
# Get article information as XML files for a PubMed id
xmls <- pubmed(names(xx)[1], disp = "data")
# View article information using a browser
pubmed(names(xx)[1], disp = "browser")
}
}
Results
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(illuminaMousev1p1.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.Mm.eg.db
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/illuminaMousev1p1.db/illuminaMousev1p1PMID.Rd_%03d_medium.png", width=480, height=480)
> ### Name: illuminaMousev1p1PMID
> ### Title: Maps between Manufacturer Identifiers and PubMed Identifiers
> ### Aliases: illuminaMousev1p1PMID illuminaMousev1p1PMID2PROBE
> ### Keywords: datasets
>
> ### ** Examples
>
> x <- illuminaMousev1p1PMID
> # Get the probe identifiers that are mapped to any PubMed ID
> mapped_probes <- mappedkeys(x)
> # Convert to a list
> xx <- as.list(x[mapped_probes])
> if(length(xx) > 0){
+ # Get the PubMed identifiers for the first two probe identifiers
+ xx[1:2]
+ # Get the first one
+ xx[[1]]
+ # if(interactive() && !is.null(xx[[1]]) && !is.na(xx[[1]])
+ && require(annotate)){
Error: unexpected '&&' in:
"# if(interactive() && !is.null(xx[[1]]) && !is.na(xx[[1]])
&&"
Execution halted