Maintainer: Levi Waldron <lwaldron.research@gmail.com>
Depends: R (≥ 4.1.0), methods, utils
Version: 0.8.15
Date: 2024-11-16
License: GPL-2 | GPL-3 [expanded from: GPL (≥ 2.0)]
Title: Identify and Correct Invalid HGNC Human Gene Symbols and MGI Mouse Gene Symbols
Description: Contains functions for identifying and correcting HGNC human gene symbols and MGI mouse gene symbols which have been converted to date format by Excel, withdrawn, or aliased. Also contains functions for reversibly converting between HGNC symbols and valid R names.
URL: https://github.com/waldronlab/HGNChelper, https://waldronlab.io/HGNChelper/
BugReports: https://github.com/waldronlab/HGNChelper/issues
LazyData: TRUE
RoxygenNote: 7.3.2
Encoding: UTF-8
Imports: splitstackshape
Suggests: testthat, knitr, rmarkdown, markdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-11-16 16:08:43 UTC; Levi
Author: Sehyun Oh [aut], Ayush Aggarwal [aut], Markus Riester [aut], Levi Waldron [aut, cre]
Repository: CRAN
Date/Publication: 2024-11-16 17:10:11 UTC

HGNChelper: Identify and Correct Invalid HGNC Human Gene Symbols and MGI Mouse Gene Symbols

Description

Contains functions for identifying and correcting HGNC human gene symbols and MGI mouse gene symbols which have been converted to date format by Excel, withdrawn, or aliased. Also contains functions for reversibly converting between HGNC symbols and valid R names.

Author(s)

Maintainer: Levi Waldron lwaldron.research@gmail.com

Authors:

See Also

Useful links:

Title function to convert Affymetrix probeset identifiers to valid R names

Description

This function simply prepends "affy." to the probeset IDs to create valid R names. Reverse operation is done by the rToAffy function.

Usage

affyToR(x)

Arguments

x

vector of Affymetrix probeset identifiers, or any identifier which may with a digit.

Value

a character vector that is simply x with "affy." prepended to each value.

Identify outdated or Excel-mogrified gene symbols

Description

This function identifies gene symbols which are outdated or may have been mogrified by Excel or other spreadsheet programs. If output is assigned to a variable, it returns a data.frame of the same number of rows as the input, with a second column indicating whether the symbols are valid and a third column with a corrected gene list.

Usage

checkGeneSymbols(
  x,
  chromosome = NULL,
  unmapped.as.na = TRUE,
  map = NULL,
  species = "human",
  expand.ambiguous = FALSE
)

Arguments

x

A character vector of gene symbols to check for modified or outdated values

chromosome

An optional integer vector containing the chromosome number of each gene provided through the argument x. It should be the same length as the input for x. Currently, this argument is implemented only for human gene cases.

unmapped.as.na

If TRUE (default), unmapped symbols will appear as NA in the Suggested.Symbol column. If FALSE, the original unmapped symbol will be kept.

map

Specify if you do not want to use the default maps provided by setting species equal to "mouse" or "human". Map can be any other data.frame with colnames identical to c("Symbol", "Approved.Symbol"). The default maps can be updated by running the interactive example below.

species

A character vector of length 1, either "human" (default) or "mouse". If NULL, or anything other than "human" or "mouse", then the map argument must be provided.

expand.ambiguous

If FALSE (default), genes with multiple mapping will only map to its approved symbol as the correct one. If TRUE, genes with multiple/ambiguous mapping will map to all the symbols linked to it.

Value

The function will return a data.frame of the same number of rows as the input, with corrections possible from map.

See Also

mouse.table for the mouse lookup table, hgnc.table for the human lookup table

Examples

library(HGNChelper)

## Human
human <- c("FN1", "TP53", "UNKNOWNGENE","7-Sep", "9/7", "1-Mar", "Oct4", "4-Oct",
      "OCT4-PG4", "C19ORF71", "C19orf71")
checkGeneSymbols(human)

## Mouse
mouse <- c("1-Feb", "Pzp", "A2m")
checkGeneSymbols(mouse, species="mouse")

## expand.ambiguous

## Human
human <- "AAVS1"
checkGeneSymbols(human, expand.ambiguous=FALSE)
checkGeneSymbols(human, expand.ambiguous=TRUE)

## Mouse
mouse <- c("Cpamd8", "Mug2")
checkGeneSymbols(mouse, species = "mouse", expand.ambiguous = FALSE)
checkGeneSymbols(mouse, species = "mouse", expand.ambiguous = TRUE)

## Updating the map
if (interactive()) {
    currentHumanMap <- getCurrentHumanMap()
    checkGeneSymbols(human, map=currentHumanMap)

    # You should save this if you are going to use it multiple times,   
    # then load it from file rather than burdening HGNC's servers.
    save(hgnc.table, file="hgnc.table.rda", compress="bzip2")
    load("hgnc.table.rda")
    checkGeneSymbols(human, map=hgnc.table)
}

Title function to identify Excel-mogrified gene symbols

Description

This function identifies gene symbols which may have been mogrified by Excel or other spreadsheet programs. If output is assigned to a variable, it returns a vector of the same length where symbols which could be mapped have been mapped.

Usage

findExcelGeneSymbols(
  x,
  mog.map = read.csv(system.file("extdata/mog_map.csv", package = "HGNChelper"), as.is =
    TRUE),
  regex = "impossibletomatch^"
)

Arguments

x

Vector of gene symbols to check for mogrified values

mog.map

Map of known mogrifications. This should be a dataframe with two columns: original and mogrified, containing the correct and incorrect symbols, respectively.

regex

Regular expression, recognized by the base::grep function which is called with ignore.case=TRUE, to identify mogrified symbols. The default regex will not match anything. The regex in the examples is an attempt to match all Excel-mogrified HGNC human gene symbols. It is not necessary for all matches to have a corresponding entry in mog.map$mogrified; values in x which are matched by this regex but are not found in mog.map$mogrified simply will not be corrected.

Value

if the return value of the function is assigned to a variable, the function will return a vector of the same length as the input, with corrections possible from mog.map made.

Examples

## Available maps from this package:
human <- read.csv(system.file("extdata/mog_map.csv", 
                              package = "HGNChelper"), as.is=TRUE)
mouse <- read.csv(system.file("extdata/HGNChelper_mog_map_MGI_AMC_2016_03_30.csv", 
                              package = "HGNChelper"), as.is=TRUE)
## This regex is based that provided by Zeeberg et al.,
##  Mistaken Identifiers: Gene name errors can be introduced
## inadvertently when using Excel in bioinformatics.  BMC
##  Bioinformatics 2004, 5:80.
re <- "[0-9]\\-(JAN|FEB|MAR|APR|MAY|JUN|JUL|AUG|SEP|OCT|NOV|DEC)|[0-9]\\.[0-9][0-9]E\\+[[0-9][0-9]"
findExcelGeneSymbols(c("2-Apr", "APR2"), mog.map=human, regex=re)
findExcelGeneSymbols(c("1-Feb", "Feb1"), mog.map=mouse)

Get the current maps for correcting gene symbols

Description

Valid human and mouse gene symbols can be updated frequently. Use these functions to get the most current lists of valid symbols, which you can then use as an input to the map argument of checkGeneSymbols. Make sure to change the default species="human" argument to checkGeneSymbols if you are doing this for mouse. Use getCurrentHumanMap for HGNC human gene symbols from https://www.genenames.org/ and getCurrentMouseMap for MGI mouse gene symbols from https://www.informatics.jax.org/downloads/reports/MGI_EntrezGene.rpt.

Usage

getCurrentHumanMap()
getCurrentMouseMap()

Value

A data.frame that can be used for map argument of checkGeneSymbols function

Examples

## Not run: 
## human
new.hgnc.table <- getCurrentHumanMap()
checkGeneSymbols(c("3-Oct", "10-3", "tp53"), map=new.hgnc.table)

## mouse
new.mouse.table <- getCurrentMouseMap()
## Set species to NULL or "mouse" 
checkGeneSymbols(c("Gm46568", "1-Feb"), map=new.mouse.table, species="mouse")

## End(Not run)

All current and withdrawn HGNC gene symbols and Excel-mogrified symbols

Description

A data.frame with the first column providing a gene symbol or known alias (including withdrawn symbols), second column providing the approved HGNC human gene symbol.

Usage

hgnc.table

Format

An object of class data.table (inherits from data.frame) with 103939 rows and 3 columns.

Source

Extracted from https://storage.googleapis.com/public-download-files/hgnc/tsv/tsv/hgnc_complete_set.txt and system.file("extdata/mog_map.csv", package="HGNChelper")

Examples

data("hgnc.table", package="HGNChelper")
head(hgnc.table)

All current and withdrawn MGI mouse symbols and Excel-mogrified symbols

Description

A data.frame with the first column providing a gene symbol or known alias (including withdrawn symbols), second column providing the approved MGI mouse gene symbol.

Usage

mouse.table

Format

An object of class data.frame with 790110 rows and 2 columns.

Source

Extracted from http://www.informatics.jax.org/downloads/reports/MGI_EntrezGene.rpt and system.file("extdata/HGNChelper_mog_map_MGI_AMC_2016_03_30.csv", package="HGNChelper")

Examples

data("mouse.table", package="HGNChelper")
head(mouse.table)

Title function to convert the output of affyToR back to the original Affymetrix probeset identifiers.

Description

This function simply strips the "affy." added by the affyToR function.

Usage

rToAffy(x)

Arguments

x

the character vector returned by the affyToR function.

Value

a character vector of Affymetrix probeset identifiers.

Title function to reverse the conversion made by symbolToR

Description

This function reverses the actions of the symbolToR function.

Usage

rToSymbol(x)

Arguments

x

the character vector returned by the symbolToR function.

Value

a character vector of HGNC gene symbols, which are not in general valid R names.

See Also

symbolToR

Title function to *reversibly* convert HGNC gene symbols to valid R names.

Description

This function reversibly converts HGNC gene symbols to valid R names by prepending "symbol.", and making the following substitutions: "-" to "hyphen", "@" to "ampersand", and "/" to "forwardslash".

Usage

symbolToR(x)

Arguments

x

vector of HGNC symbols

Value

a vector of valid R names, of the same length as x, which can be converted to the same HGNC symbols using the rToSymbol function.

See Also

rToSymbol

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