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("ShixiangWang/IDConverter")Or Gitee (better in China, but not updated anymore):
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 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.
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")
#> [1] "ENSG00000141510" "ENSG00000133703" "ENSG00000146648" "ENSG00000136997"
# Or use data from annotables
ls_annotables()
#> 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")
head(grch37)
#> ensgene entrez symbol chr start end strand biotype
#> 1 ENSG00000000003 7105 TSPAN6 X 100627108 100639991 -1 protein_coding
#> 2 ENSG00000000005 64102 TNMD X 100584936 100599885 1 protein_coding
#> 3 ENSG00000000419 8813 DPM1 20 50934867 50959140 -1 protein_coding
#> 4 ENSG00000000457 57147 SCYL3 1 169849631 169894267 -1 protein_coding
#> 5 ENSG00000000460 55732 C1orf112 1 169662007 169854080 1 protein_coding
#> 6 ENSG00000000938 2268 FGR 1 27612064 27635185 -1 protein_coding
#> description
#> 1 tetraspanin 6
#> 2 tenomodulin
#> 3 dolichyl-phosphate mannosyltransferase subunit 1, catalytic
#> 4 SCY1 like pseudokinase 3
#> 5 chromosome 1 open reading frame 112
#> 6 FGR proto-oncogene, Src family tyrosine kinase
convert_custom(c("TP53", "KRAS", "EGFR", "MYC"),
from = "symbol", to = "entrez", dt = grch37)
#> [1] "7157" "3845" "1956" "4609"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
- AnnoProbe (Gitee mirror) is an R package for transforming Chips probes to different Gene IDs.
MIT@2020, Shixiang Wang