Skip to contents

Crosswalks for MGI markers

Source: R/mapping.R
update_symbol.Rd

Crosswalks involving MGI gene symbols, identifiers, Entrez gene identifiers and Ensembl gene identifiers.

Usage

update_symbol(symbol)

symbol_to_marker_id(symbol)

marker_id_to_ensembl_id(marker_id)

ensembl_id_to_marker_id(ensembl_id)

marker_id_to_entrez_id(marker_id)

entrez_id_to_marker_id(entrez_id)

symbol_to_ensembl_id(symbol)

marker_id_to_symbol(marker_id)

ensembl_id_to_symbol(ensembl_id)

symbol_to_entrez_id(symbol)

Arguments

symbol

A character vector of marker symbols.

marker_id

A character vector of MGI marker identifiers.

ensembl_id

A character vector of Ensembl gene identifiers.

entrez_id

A character vector of Entrez gene identifiers.

Value

A character of mapped marker symbols or identifiers (as of 27 May 2024).

Details

Mappings to Entrez or Ensembl gene identifiers are provided only when these identifiers were valid at 27 May 2024, in other words, mappings to identifiers that have been deprecated results in NA.

  • update_symbol() maps (potentially old) symbols to most up-to-date symbols.

  • symbol_to_marker_id() maps (potentially old) symbols to marker identifiers.

  • symbol_to_ensembl_id() maps (potentially old) symbols to Ensembl identifiers.

  • symbol_to_entrez_id() maps (potentially old) symbols to Entrez gene identifiers.

  • marker_id_to_symbol() maps MGI gene markers identifiers to marker symbols.

  • marker_id_to_ensembl_id() maps MGI gene markers identifiers to an Ensembl gene identifiers.

  • marker_id_to_entrez_id() maps MGI gene markers identifiers to an Entrez gene identifiers.

  • ensembl_id_to_marker_id() maps Ensembl gene identifiers to MGI gene markers identifiers.

  • ensembl_id_to_symbol() maps Ensembl gene identifiers to marker symbols.

  • entrez_id_to_marker_id() maps Entrez gene identifiers to MGI gene markers identifiers.

Examples

symbols <- c(
"Xkr4",
"LOC102640625",
"sid2057",
"Sox17",
"ENSMUSG00000074760",
"R75157",
"6430567E01Rik",
"VINAS"
)

# Current MGI marker symbols as of 2024-05-27.
update_symbol(symbols)
#> [1] "Xkr4"          NA              "1110004F10Rik" "Sox17"        
#> [5] "1700010L13Rik" "Zyx"           "Zzz3"          "1500026H17Rik"

# Map MGI marker symbols to marker identifiers.
symbol_to_marker_id(symbols)
#> [1] "MGI:3528744" NA            "MGI:1929274" "MGI:107543"  "MGI:1922878"
#> [6] "MGI:103072"  "MGI:1920453" "MGI:1916252"

# Map MGI marker symbols to Ensembl identifiers.
symbol_to_ensembl_id(symbols)
#> [1] "ENSMUSG00000051951" NA                   "ENSMUSG00000030663"
#> [4] "ENSMUSG00000025902" NA                   "ENSMUSG00000029860"
#> [7] "ENSMUSG00000039068" "ENSMUSG00000097383"

# Map MGI marker symbols to Entrez identifiers.
symbol_to_entrez_id(symbols)
#> [1] "497097" NA       "56372"  "20671"  NA       "22793"  "108946" "69002" 

# Deprecated Ensembl identifier, e.g. 1700010L13Rik (MGI:1922878) should map
# to ENSMUSG00000074760.
# URL: https://www.informatics.jax.org/marker/MGI:1922878
symbol_to_marker_id("1700010L13Rik")
#> [1] "MGI:1922878"

# But results in `NA` because ENSMUSG00000074760 has status Retired:
# URL: https://www.ensembl.org/Mus_musculus/Gene/Idhistory?g=ENSMUSG00000074760
symbol_to_ensembl_id("1700010L13Rik")
#> [1] NA