In ShixiangWang/IDConverter: Convert Identifiers in Biological Databases

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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

PCAWG

x <- convert_pcawg("SP1677")
x

ICGC

x <- convert_icgc("SP29019")
x

Genes

convert_hm_genes(c("TP53", "KRAS", "EGFR", "MYC"), type = "symbol")

# Or use data from annotables
ls_annotables()
grch37 = load_data("grch37")
head(grch37)
convert_custom(c("TP53", "KRAS", "EGFR", "MYC"),
               from = "symbol", to = "entrez", dt = grch37)

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.