GeneConvert: Gene ID conversion function using biomart

In zh542370159/SCP: Single Cell Pipeline

Gene ID conversion function using biomart

Description

This function can convert different gene ID types within one species or between two species using the biomart service.

Usage

GeneConvert(
  geneID,
  geneID_from_IDtype = "symbol",
  geneID_to_IDtype = "entrez_id",
  species_from = "Homo_sapiens",
  species_to = NULL,
  Ensembl_version = 103,
  biomart = NULL,
  mirror = NULL,
  max_tries = 5
)

Arguments

geneID	A vector of the geneID character.
geneID_from_IDtype	Gene ID type of the input geneID. e.g. "symbol", "ensembl_id", "entrez_id"
geneID_to_IDtype	Gene ID type(s) to convert to. e.g. "symbol", "ensembl_id", "entrez_id"
species_from	Latin names for animals of the input geneID. e.g. "Homo_sapiens","Mus_musculus"
species_to	Latin names for animals of the output geneID. e.g. "Homo_sapiens","Mus_musculus"
Ensembl_version	Ensembl database version. If NULL, use the current release version.
biomart	The name of the BioMart database that you want to connect to. Possible options include "ensembl", "protists_mart", "fungi_mart", and "plants_mart".
mirror	Specify an Ensembl mirror to connect to. The valid options here are 'www', 'uswest', 'useast', 'asia'.
max_tries	The maximum number of attempts to connect with the BioMart service.

Value

A list with the following elements:

• geneID_res: A data.frame contains the all gene IDs mapped in the database with columns: 'from_IDtype','from_geneID','to_IDtype','to_geneID'

• geneID_collapse: The data.frame contains all the successfully converted gene IDs, and the output gene IDs are collapsed into a list. As a result, the 'from_geneID' column (which is set as the row names) of the data.frame is unique.

• geneID_expand: The data.frame contains all the successfully converted gene IDs, and the output gene IDs are expanded.

• Ensembl_version: Ensembl database version.

• Datasets: Datasets available in the selected BioMart database.

• Attributes: Attributes available in the selected BioMart database.

• geneID_unmapped: A character vector of gene IDs that are unmapped in the database.

Examples

res <- GeneConvert(
  geneID = c("CDK1", "MKI67", "TOP2A", "AURKA", "CTCF"),
  geneID_from_IDtype = "symbol",
  geneID_to_IDtype = "entrez_id",
  species_from = "Homo_sapiens",
  species_to = "Mus_musculus",
  Ensembl_version = 103
)
str(res)

# Convert the human genes to mouse homologs and replace the raw counts in a Seurat object.
data("pancreas_sub")
counts <- pancreas_sub@assays$RNA@counts
res <- GeneConvert(
  geneID = rownames(counts),
  geneID_from_IDtype = "symbol",
  geneID_to_IDtype = "symbol",
  species_from = "Mus_musculus",
  species_to = "Homo_sapiens",
  Ensembl_version = 103
)
# Check the number of input and converted gene IDs
input_genes <- length(rownames(counts))
db_genes <- length(unique(res$geneID_res$from_geneID))
converted_genes_input <- length(unique(res$geneID_collapse$from_geneID))
converted_genes_output <- length(unique(res$geneID_expand$symbol))
cat("Number of input gene IDs:", input_genes, "\n")
cat("Number of gene IDs mapped in the database:", db_genes, "\n")
cat("Number of input gene IDs that were successfully converted:", converted_genes_input, "\n")
cat("Number of converted gene IDs:", converted_genes_output, "\n")

homologs_counts <- aggregate(
  x = counts[res$geneID_expand[, "from_geneID"], ],
  by = list(res$geneID_expand[, "symbol"]), FUN = sum
)
rownames(homologs_counts) <- homologs_counts[, 1]
homologs_counts <- as(as_matrix(homologs_counts[, -1]), "dgCMatrix")
homologs_counts

zh542370159/SCP documentation built on Nov. 22, 2023, 2:34 a.m.