Package 'homologene'

Attempt to automatically translate a gene list

Description

Given a list of query gene list and a target gene list, the function tries find the homology pairing that matches the query list to the target list. The query list is a short list of genes while the target list is supposed to represent a large number of genes from the target species. The default output will be the largest possible list. If returnAllPossible = TRUE then all possible pairings with any matches are returned. It is possible to limit the search by setting possibleOrigins and possibleTargets. Note that gene symbols of some species are more similar to each other than others. Using this with small gene lists and without providing any possibleOrigins or possibleTargets might return multiple hits, or if returnAllPossible = TRUE a wrong match can be returned.

Usage

autoTranslate(
  genes,
  targetGenes,
  possibleOrigins = NULL,
  possibleTargets = NULL,
  returnAllPossible = FALSE,
  db = homologene::homologeneData
)

Arguments

genes	A list of genes to match the target. Symbols or NCBI ids
targetGenes	The target list. This list is supposed to represent a large number of genes from the target species.
possibleOrigins	Taxonomic identifiers of possible origin species
possibleTargets	Taxonomic identifiers of possible target species
returnAllPossible	if TRUE returns all possible pairings with non zero gene matches. If FALSE (default) returns the best match
db	Homologene database to use.

Value

A data frame if returnAllPossibe = FALSE and a list of data frames if TRUE

---

Query DIOPT database

Description

Query DIOPT database (https://www.flyrnai.org/cgi-bin/DRSC_orthologs.pl) for orthologues. DIOPT database uses multiple tools to find gene orthologues. Sadly they don't have an API so this function queries by visiting the site and filling up the form. By default each query will take a minimum of 10 seconds due to delay parameter. This is taken from their robots.txt at the time this function is written. Note that DIOPT is not necesariy in sync with homologene database as provided in this package.

Usage

diopt(genes, inTax, outTax, delay = 10)

Arguments

genes	A vector of gene identifiers. Anything that DIOPT accepts
inTax	taxid of the species that the input genes are coming from
outTax	taxid of the species that you are seeking homology. 0 to query all species.
delay	How many seconds of delay should be between queries. Default is 10 based on the robots.txt at the time this function is written.

Details

DIOPT does not support all species available in the homologene database. The supported species are:

4896

Schizosaccharomyces pombe

4932

Saccharomyces cerevisiae

6239

Caenorhabditis elegans

7227

Drosophila melanogaster

7955

Danio rerio

8364

Xenopus (Silurana) tropicalis

9606

Homo sapiens

10090

Mus musculus

10116

Rattus norvegicus

3702

Arabidopsis thaliana

Value

A data frame

---

Download gene history file

Description

Downloads and reads the gene history file from NCBI website. This file is needed for other functions

Usage

getGeneHistory(destfile = NULL, justRead = FALSE)

Arguments

destfile	Path of the output file. If NULL a temp file will be used
justRead	If TRUE and destfile exists, it reads the file instead of downloading the latest one from NCBI

Value

A data frame with latest gene history information

---

Download gene symbol information

Description

This function downloads the gene_info file from NCBI website and returns the gene symbols for current IDs.

Usage

getGeneInfo(destfile = NULL, justRead = FALSE, chunk_size = 1e+06)

Arguments

destfile	Path of the output file. If NULL a temp file will be used
justRead	If TRUE and destfile exists, it reads the file instead of downloading the latest one from NCBI
chunk_size	Chunk size to be used with link[readr]{read_tsv_chunked}. The gene_info file is big enough to make its intake difficult. If you don't have large amounts of free memory you may have to reduce this number to read the file in smaller chunks

Value

A data frame with gene symbols for each current gene id

---

Get the latest homologene file

Description

This function downloads the latest homologene file from NCBI. Note that Homologene has not been updated since 2014 so the output will be identical to homologeneData included in this package. This function is here for futureproofing purposes.

Usage

getHomologene(destfile = NULL, justRead = FALSE)

Arguments

destfile	Path of the output file. If NULL a temp file will be used
justRead	If TRUE and destfile exists, it reads the file instead of downloading the latest one from NCBI

Value

A data frame with homology groups, gene ids and gene symbols

---

Get homologues of given genes

Description

Given a list of genes and a taxid, returns a data frame inlcuding the genes and their corresponding homologues

Usage

homologene(genes, inTax, outTax, db = homologene::homologeneData)

Arguments

genes	A vector of gene symbols or NCBI ids
inTax	taxid of the species that the input genes are coming from
outTax	taxid of the species that you are seeking homology
db	Homologene database to use.

Examples

homologene(c('Eno2','17441'), inTax = 10090, outTax = 9606)

---

homologeneData

Description

List of gene homologues used by homologene functions

Usage

homologeneData

Format

An object of class data.frame with 275237 rows and 4 columns.

---

homologeneData2

Description

A modified copy of the homologene database. Homologene was updated at 2014 and many of its gene IDs and symbols are out of date. Here the IDs and symbols are replaced with their most current version Last update: Tue Oct 31 18:41:52 2023

Usage

homologeneData2

Format

An object of class data.frame with 266573 rows and 4 columns.

---

Version of homologene used

Description

Version of homologene used

Usage

homologeneVersion

Format

An object of class integer of length 1.

---

Human/mouse wraper for homologene

Description

Human/mouse wraper for homologene

Usage

human2mouse(genes, db = homologene::homologeneData)

Arguments

genes	A vector of gene symbols or NCBI ids
db	Homologene database to use.

Examples

human2mouse(c('ENO2','4340'))

---

Mouse/human wraper for homologene

Description

Mouse/human wraper for homologene

Usage

mouse2human(genes, db = homologene::homologeneData)

Arguments

genes	A vector of gene symbols or NCBI ids
db	Homologene database to use.

Examples

mouse2human(c('Eno2','17441'))

---

Names and ids of included species

Description

Names and ids of included species

Usage

taxData

Format

An object of class data.frame with 21 rows and 2 columns.

---

Update homologene database

Description

Creates an updated version of the homologene database. This is done by downloading the latest gene annotation information and tracing changes in gene symbols and identifiers over history. homologeneData2 was created using this function over the original homologeneData. This function requires downloading large amounts of data from the NCBI ftp servers.

Usage

updateHomologene(
  destfile = NULL,
  baseline = homologene::homologeneData2,
  gene_history = NULL,
  gene_info = NULL
)

Arguments

destfile	Optional. Path of the output file.
baseline	The baseline homologene file to be used. By default uses the homologeneData2 that is included in this package. The more ids to update, the more time is needed for the update which is why the default option uses an already updated version of the original database.
gene_history	A gene history data frame, possibly returned by getGeneHistory function. Use this if you want to have a static gene_history file to update up to a specific date. An up to date gene_history object can be set to update to a specific date by trimming rows that have recent dates. Note that the same is not possible for the gene_info If not provided, the latest file will be downloaded.
gene_info	A gene info data frame that contatins ID-symbol matches, possibly returned by getGeneInfo. Use this if you want a static version. Should be in sync with the gene_history file. Note that there is no easy way to track changes in gene symbols back in time so if you want to update it up to a specific date, make sure you don't lose that file.

Value

Homologene database in a data frame with updated gene IDs and symbols

---

Update gene IDs

Description

Given a list of gene ids and gene history information, traces changes in the gene's name to get the latest valid ID

Usage

updateIDs(ids, gene_history)

Arguments

ids	Gene ids
gene_history	Gene history information, probably returned by getGeneHistory

Value

A character vector. New ids for genes that changed ids, or "-" for discontinued genes. the input itself.

Examples

## Not run: 
gene_history = getGeneHistory()
updateIDs(c("4340964", "4349034", "4332470", "4334151", "4323831"),gene_history)

## End(Not run)

---