README.md

In ShixiangWang/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

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")

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")
x
#> [1] "TCGA-02-0001"

PCAWG

x <- convert_pcawg("SP1677")
x
#> [1] "DO804"

ICGC

x <- convert_icgc("SP29019")
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()
#> 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"

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

ShixiangWang/IDConverter documentation built on Aug. 24, 2023, 9:54 p.m.