The goal of IDConverter is to convert identifiers between biological databases. Currently, I mainly use it for promoting cancer study.
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")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)
#> # 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"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