# Getting Started with IDConverter

## Overview

IDConverter converts identifiers within and between biological databases. Core use cases:

- TCGA/ICGC/PCAWG sample ID conversion
- Human ↔︎ Mouse gene ortholog mapping
- Gene symbol ↔︎ Ensembl ID conversion
- Gene alias resolution
- GDC manifest parsing and tumor-normal pairing

## ID Conversion

    library(IDConverter)

    # TCGA sample ID → patient ID
    convert_tcga("TCGA-02-0001-10")
    #> [1] "TCGA-02-0001"

    # ICGC specimen → donor
    convert_icgc("SP29019")
    #> [1] "DO13695"

    # PCAWG specimen → donor
    convert_pcawg("SP1677")
    #> [1] "DO804"

## Gene ID Conversion

    # Symbol → Ensembl (human)
    convert_hm_genes(c("TP53", "KRAS"), type = "symbol")

    # Ensembl → Symbol (human)
    convert_hm_genes("ENSG00000141510")

    # Human → Mouse orthologs
    convert_hm_orthologs(c("TP53", "KRAS"))

## Gene Annotation Tables

    # List available tables
    ls_annotables()

    # Load from Zenodo (fixed version, works offline)
    grch38 <- load_data("grch38")

    # Or build from Ensembl BioMart (latest, requires biomaRt + internet)
    grch38_latest <- build_annotables("grch38", tx2gene = FALSE)

## Working with Custom Databases

    dt <- data.table::data.table(
      UpperCase = LETTERS[1:5],
      LowerCase = letters[1:5]
    )
    convert_custom(c("B", "C", "E"), from = "UpperCase", to = "LowerCase", dt = dt)
    #> [1] "b" "c" "e"