IDConverter
The goal of IDConverter is to convert identifiers between biological databases. Currently, I mainly use it for promoting cancer study.
Installation
You can install the released version of IDConverter from CRAN with:
install.packages("IDConverter")Or install the latest version of IDConverter in GitHub with:
remotes::install_github("ShixiangWang/IDConverter")Or Gitee (better in China):
remotes::install_git("https://gitee.com/ShixiangWang/IDConverter")Available features
ID conversions:
convert_custom()- Convert custom database identifiers.convert_icgc()- Convert ICGC identifiers.convert_pcawg()- Convert PCAWG identifiers.convert_tcga()- Convert TCGA identifiers.convert_hm_genes()- Convert human/mouse gene IDs between Ensembl and Hugo Symbol system.
Annotation tables from
annotables are available
in this package, you can use ls_annotables() to print the table list
and then use load_data() to download and load the data into R for
conversion operation.
Others:
parse_gdc_file_uuid()- Parse Metadata from GDC Portal File UUID.filter_tcga_barcodes()- Filter TCGA Replicate Sample Barcodes.
Examples
library(IDConverter)To follow the CRAN policy, I have to set tempdir() as default data
path, however, I recommend you set the data path to a specified path
with options(IDConverter.datapath).
e.g.,
options(IDConverter.datapath = system.file("extdata", package = "IDConverter"))TCGA
x <- convert_tcga("TCGA-02-0001-10")
#> Downloading https://zenodo.org/record/6342397/files/tcga.rda to /Users/wsx/Library/R/IDConverter/extdata/tcga.rda
x
#> [1] "TCGA-02-0001"PCAWG
x <- convert_pcawg("SP1677")
#> Downloading https://zenodo.org/record/6342397/files/pcawg_full.rda to /Users/wsx/Library/R/IDConverter/extdata/pcawg_full.rda
x
#> [1] "DO804"ICGC
x <- convert_icgc("SP29019")
#> Downloading https://zenodo.org/record/6342397/files/icgc.rda to /Users/wsx/Library/R/IDConverter/extdata/icgc.rda
x
#> [1] "DO13695"Genes
convert_hm_genes(c("TP53", "KRAS", "EGFR", "MYC"), type = "symbol")
#> [1] "ENSG00000141510" "ENSG00000133703" "ENSG00000146648" "ENSG00000136997"
# Or use data from annotables
ls_annotables()
#> Downloading https://zenodo.org/record/6342397/files/ensembl_version.rda to /Users/wsx/Library/R/IDConverter/extdata/ensembl_version.rda
#> Version: Ensembl Genes 105
#> [1] "bdgp6" "bdgp6_tx2gene" "galgal5" "galgal5_tx2gene"
#> [5] "grch37" "grch37_tx2gene" "grch38" "grch38_tx2gene"
#> [9] "grcm38" "grcm38_tx2gene" "mmul801" "mmul801_tx2gene"
#> [13] "rnor6" "rnor6_tx2gene" "wbcel235" "wbcel235_tx2gene"
grch37 = load_data("grch37")
#> Downloading https://zenodo.org/record/6342397/files/grch37.rda to /Users/wsx/Library/R/IDConverter/extdata/grch37.rda
head(grch37)
#> # A tibble: 6 × 9
#> ensgene entrez symbol chr start end strand biotype descr…¹
#> <chr> <int> <chr> <chr> <int> <int> <int> <chr> <chr>
#> 1 ENSG00000000003 7105 TSPAN6 X 100627108 1.01e8 -1 protei… tetras…
#> 2 ENSG00000000005 64102 TNMD X 100584936 1.01e8 1 protei… tenomo…
#> 3 ENSG00000000419 8813 DPM1 20 50934867 5.10e7 -1 protei… dolich…
#> 4 ENSG00000000457 57147 SCYL3 1 169849631 1.70e8 -1 protei… SCY1 l…
#> 5 ENSG00000000460 55732 C1orf112 1 169662007 1.70e8 1 protei… chromo…
#> 6 ENSG00000000938 2268 FGR 1 27612064 2.76e7 -1 protei… FGR pr…
#> # … with abbreviated variable name ¹description
convert_custom(c("TP53", "KRAS", "EGFR", "MYC"),
from = "symbol", to = "entrez", dt = grch37)
#> [1] "7157" "3845" "1956" "4609"Citation
Wang S, Li H, Song M, Tao Z, Wu T, He Z, et al. (2021) Copy number signature analysis tool and its application in prostate cancer reveals distinct mutational processes and clinical outcomes. PLoS Genet 17(5): e1009557. https://doi.org/10.1371/journal.pgen.1009557
Similar package
- AnnoProbe (Gitee mirror) is an R package for transforming Chips probes to different Gene IDs.
LICENSE
MIT@2020, Shixiang Wang