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The goal of IDConverter is to convert identifiers between biological databases. Currently, I mainly use it for promoting cancer study.
Install the latest version of IDConverter in GitHub with:
remotes::install_github("WangLabCSU/IDConverter")Or Gitee (better in China, but updates may lag behind):
remotes::install_git("https://gitee.com/ShixiangWang/IDConverter")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/worm gene IDs
between Ensembl and Hugo Symbol system.convert_hm_orthologs() - Convert gene IDs between human
and mouse via Ensembl orthology (e.g., TP53 ↔︎ Trp53).Annotation tables:
ls_annotables() - List available annotation tables from
annotables.load_data() - Download and load annotation data from
Zenodo (fixed version) or from local cache.build_annotables() - Build up-to-date gene annotation
tables directly from Ensembl BioMart (supports 11 organisms, requires
biomaRt).resolve_gene_aliases() - Resolve outdated/alternative
gene symbols (aliases) to official symbols via Ensembl synonym
data.Utilities:
pair_gdc_samples() - Pair tumor-normal samples from GDC
manifest files.parse_gdc_file_uuid() - Parse Metadata from GDC Portal
File UUID.filter_tcga_barcodes() - Filter TCGA Replicate Sample
Barcodes.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"))x <- convert_tcga("TCGA-02-0001-10")
x
#> [1] "TCGA-02-0001"x <- convert_pcawg("SP1677")
x
#> [1] "DO804"x <- convert_icgc("SP29019")
x
#> [1] "DO13695"convert_hm_genes(c("TP53", "KRAS", "EGFR", "MYC"), type = "symbol")
#> Downloading https://zenodo.org/records/10360995/files/human_hg38_gene_info.rds to /private/var/folders/1w/371ktd8j0fv8mp_dsgtvssnw0000gn/T/RtmpMMmC4n/temp_libpath4f1e764f17f3/IDConverter/extdata/human_hg38_gene_info.rds
#> [1] "ENSG00000141510" "ENSG00000133703" "ENSG00000146648" "ENSG00000136997"
# Or use data from annotables
ls_annotables()
#> Downloading https://zenodo.org/records/10360995/files/ensembl_version.rda to /private/var/folders/1w/371ktd8j0fv8mp_dsgtvssnw0000gn/T/RtmpMMmC4n/temp_libpath4f1e764f17f3/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/records/10360995/files/grch37.rda to /private/var/folders/1w/371ktd8j0fv8mp_dsgtvssnw0000gn/T/RtmpMMmC4n/temp_libpath4f1e764f17f3/IDConverter/extdata/grch37.rda
head(grch37)
#> # A tibble: 6 × 9
#> ensgene entrez symbol chr start end strand biotype description
#> <chr> <int> <chr> <chr> <int> <int> <int> <chr> <chr>
#> 1 ENSG00000000003 7105 TSPAN6 X 1.01e8 1.01e8 -1 protei… tetraspani…
#> 2 ENSG00000000005 64102 TNMD X 1.01e8 1.01e8 1 protei… tenomodulin
#> 3 ENSG00000000419 8813 DPM1 20 5.09e7 5.10e7 -1 protei… dolichyl-p…
#> 4 ENSG00000000457 57147 SCYL3 1 1.70e8 1.70e8 -1 protei… SCY1 like …
#> 5 ENSG00000000460 55732 C1orf112 1 1.70e8 1.70e8 1 protei… chromosome…
#> 6 ENSG00000000938 2268 FGR 1 2.76e7 2.76e7 -1 protei… FGR proto-…
convert_custom(c("TP53", "KRAS", "EGFR", "MYC"),
from = "symbol", to = "entrez", dt = grch37)
#> [1] "7157" "3845" "1956" "4609"# Human → Mouse
convert_hm_orthologs(c("TP53", "KRAS", "EGFR", "MYC"))
# => Trp53, Kras, Egfr, Myc
# Mouse → Human
convert_hm_orthologs(c("Trp53", "Kras"), from_species = "mouse", to_species = "human")
# => TP53, KRAS
# Ensembl ID mapping
convert_hm_orthologs("ENSG00000141510", from_type = "ensembl", to_type = "ensembl")
# => ENSMUSG00000059552# Build annotation table with synonym support
ann <- build_annotables("grch38", include_synonyms = TRUE, tx2gene = FALSE)
# Resolve aliases (e.g., old names → official symbols)
resolve_gene_aliases(c("TP53", "T245", "MLL"), ann[[1]])
# T245 → TSPAN6, MLL → KMT2A (if in synonym data)# Pair tumor-normal samples from a GDC manifest file
info <- pair_gdc_samples("gdc_manifest.txt")
head(info)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
MIT@2020, Shixiang Wang
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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