R: Entrez identifiers for disease-related genes in the OMIM...
omimIds
R Documentation
Entrez identifiers for disease-related genes in the OMIM database
Description
Entrez identifiers for several lists of genes related with human
disease.
diseaseIds
contains the Entrez identifiers corresponding to
disease-related genes found in the OMIM database. This list has been manually
curated by Nuria Lopez-Bigas et al. who kindly provided it to us.
morbidmapIds
contains the Entrez identifiers for all the genes
in the morbidmap table. This list would correspond to disease-related genes
if there had been no manual curation, as in the previous list
('diseaseIds').
dominantIds
ontains the Entrez identifiers for dominant genes
after manual curation by Nuria Lopez-Bigas who has kindly allowed us to
include them in the package.
recessiveIds
contains the Entrez identifiers for recessive genes
after manual curation by Nuria Lopez-Bigas who has kindly allowed us to
include them in the package.
dominantIdsEBI
contains the Entrez identifiers for dominant
genes in the EBI version of the OMIM database recovered using SRS with the
term 'dominant' in the KEYWORDS field.
recessiveIdsEBI
contains the Entrez identifiers for recessive genes in the EBI version of the OMIM database recovered using SRS with the term 'recessive' in the KEYWORDS field.
dominantIdsNCBI
contains the Entrez identifiers for dominant
genes in the NCBI version of the OMIM database recovered using ENTREZ with the
term 'dominant' in the CLINICAL field.
recessiveIdsNCBI
contains the Entrez identifiers for recessive
genes in the NCBI version of the OMIM database recovered using ENTREZ with the
term 'recessive' in the CLINICAL field.
Usage
data(omimIds)
Format
Each dataset is a character vector with a different number of elements which (should) correspond to valid Entrez identifiers
Details
Lopez-Bigas et al. analyzed the distribution of functional categories in genes causing disease in human.
They did several comparisosn which can also be done using goProfiles. In order to perform these comparisons
we first tried to obtain the same lists of genes using standard database browsers, such as 'SRS', at the European Bioinformatics Institute, or 'Entrez', at the National Center for Biotechnological Information. Curiously both approaches provided very different lists so we asked the authors for their data and they kindly provided them to us. In order to facilitat the use of functions included in goProfiles we have trimmed the list of recessive and dominant genes so that (i) They become exclussive (no gene belows to both lists) (2) They are both included in the diseaseIds list. This eliminated 39 genes (out of 639) from the list of recessive genes and 52 genes (out of 414) from the list of dominant genes
References
Lopez-Bigas, N., Blencowe, B.J. and Ouzounis, C.A.,
Highly consistent patterns for inherited human diseases at the molecular level,
Bioinformatics, 2006, 22 (3), 269-277.
Examples
data(omimIds)
Results
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(goProfiles)
Loading required package: Biobase
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
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: AnnotationDbi
Loading required package: stats4
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: GO.db
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/goProfiles/omimIds.Rd_%03d_medium.png", width=480, height=480)
> ### Name: omimIds
> ### Title: Entrez identifiers for disease-related genes in the OMIM
> ### database
> ### Aliases: omimIds diseaseIds morbidmapIds dominantIds recessiveIds
> ### dominantIdsEBI recessiveIdsEBI dominantIdsNCBI recessiveIdsNCBI
> ### Keywords: datasets
>
> ### ** Examples
>
> data(omimIds)
>
>
>
>
>
> dev.off()
null device
1
>