| Type: | Package |
| Title: | Gene ID Mapping for Genotype-Tissue Expression (GTEx) Data |
| Version: | 1.9 |
| Maintainer: | Nan Xiao <me@nanx.me> |
| Description: | Convert 'Ensembl' gene identifiers from Genotype-Tissue Expression (GTEx) data to identifiers in other annotation systems, including 'Entrez', 'HGNC', and 'UniProt'. |
| License: | GPL-3 | file LICENSE |
| LazyData: | TRUE |
| VignetteBuilder: | knitr |
| URL: | https://nanx.me/grex/, https://github.com/nanxstats/grex |
| BugReports: | https://github.com/nanxstats/grex/issues |
| Depends: | R (≥ 3.5.0) |
| Suggests: | knitr, rmarkdown |
| Encoding: | UTF-8 |
| RoxygenNote: | 6.1.1 |
| NeedsCompilation: | no |
| Packaged: | 2019-05-17 22:22:43 UTC; nanx |
| Author: | Nan Xiao  [aut,
cre],
Gao Wang [aut],
Lei Sun [aut] |
| Repository: | CRAN |
| Date/Publication: | 2019-05-17 22:40:04 UTC |
Remove Version Numbers in Raw GTEx (GENCODE) Gene IDs
Description
Remove the '.version' part in raw GTEx (GENCODE) gene IDs to produce Ensembl IDs.
Usage
cleanid(gtex_id)
Arguments
gtex_id |
Character vector of GTEx (GENCODE) gene IDs |
Value
Character vector of Ensembl IDs
Examples
gtex_id <- c("ENSG00000227232.4", "ENSG00000223972.4", "ENSG00000268020.2")
cleanid(gtex_id)
Gene ID Mapping for Genotype-Tissue Expression (GTEx) Data
Description
Map Ensembl IDs to Entrez Gene ID, HGNC symbol, and UniProt ID, with basic annotation information such as gene type.
Usage
grex(ensembl_id)
Arguments
ensembl_id |
Character vector of Ensembl IDs |
Value
This function returns a data frame with the same number of rows as the length of input Ensembl IDs, containing:
-
ensembl_id- Input Ensembl ID -
entrez_id- Entrez Gene ID -
hgnc_symbol- HGNC gene symbol -
hgnc_name- HGNC gene name -
cyto_loc- Cytogenetic location -
uniprot_id- UniProt ID -
gene_biotype- Gene type
The elements that cannot be mapped will be NA.
Examples
# Ensembl IDs in GTEx v6p gene count data
data("gtexv6p")
# select 100 IDs as example
id <- gtexv6p[101:200]
df <- grex(id)
# Rows that have a mapped Entrez ID
df[
!is.na(df$"entrez_id"),
c("ensembl_id", "entrez_id", "gene_biotype")
]
Ensembl IDs from GTEx V6 Gene Read Count Data
Description
A dataset containing the Ensembl IDs from GTEx (V6) gene read count data.
Usage
gtexv6
Format
A character vector with 56,318 Ensembl IDs.
Source
Ensembl IDs from GTEx V6p Gene Read Count Data
Description
A dataset containing the Ensembl IDs from GTEx (V6p) gene read count data.
Usage
gtexv6p
Format
A character vector with 56,238 Ensembl IDs.
Source
Ensembl IDs from GTEx V7 Gene Read Count Data
Description
A dataset containing the Ensembl IDs from GTEx (V7) gene read count data.
Usage
gtexv7
Format
A character vector with 56,202 Ensembl IDs.