README.md

In IDConverter: Convert Identifiers in Biological Databases

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 ¹​description
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

IDConverter documentation built on March 31, 2023, 10:25 p.m.