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| # Basic function to convert human to mouse gene names | |
| convertHumanGeneList <- function(x){ | |
| require("biomaRt") | |
| human = useMart("ensembl", dataset = "hsapiens_gene_ensembl") | |
| mouse = useMart("ensembl", dataset = "mmusculus_gene_ensembl") | |
| genesV2 = getLDS(attributes = c("hgnc_symbol"), filters = "hgnc_symbol", values = x , mart = human, attributesL = c("mgi_symbol"), martL = mouse, uniqueRows=T) | |
| humanx <- unique(genesV2[, 2]) | |
| no_mouse_genes <- length(x) | |
| no_human_genes <- length(humanx) | |
| if(no_human_genes != no_mouse_genes){ | |
| print("Some genes could not be translated!") | |
| genes_not_trans <- setdiff(x,genesV2$HGNC.symbol) | |
| print("These genes could not be translated:") | |
| print(genes_not_trans) | |
| print(paste("A total number of ",length(genes_not_trans),"genes could not be translated!"),sep=" ") | |
| }else{ | |
| print("All genes were translated successfully!") | |
| } | |
| # Print all gene names that could not be translated and the number of genes that were not translated | |
| return(humanx) | |
| } |
convert human to mouse gene names (https://gist.github.com/FloWuenne/f8fc922477df04c1642e9d8945c48d47)
humGenes <- c("HMMR", "TLX3", "CPEB4") # prepare a list of human genes needs to be converted
convertHumantoMouse <- function(x){
require("biomaRt")
human = useEnsembl(biomart = "genes", dataset = "hsapiens_gene_ensembl")
mouse = useEnsembl(biomart = "genes", dataset = "mmusculus_gene_ensembl")
genesV2 = getLDS(attributes = c("hgnc_symbol"), filters = "hgnc_symbol", values = x , mart = human, attributesL = c("mgi_symbol"), martL = mouse, uniqueRows=T)
mousex <- unique(genesV2[, 2]) # unique the 2nd column values
human_genes_number <- length(x)
mouse_genes_number <- length(mousex)
if(human_genes_number != mouse_genes_number){
genes_not_trans <- setdiff(x, genesV2$HGNC.symbol)
print("These genes could not be translated:")
print(genes_not_trans)
print(paste("A total number of ",length(genes_not_trans),"genes could not be translated!"),sep=" ")
}else{
print("All genes were translated successfully!")
}
return(mousex)
}
ConvertedGenes <- convertHumantoMouse(humGenes)
convert mouse gene to human gene (https://rjbioinformatics.com/2016/10/14/converting-mouse-to-human-gene-names-with-biomart-package/)
musGenes <- c("Hmmr", "Tlx3", "Cpeb4")
convertMousetohuman <- function(x){
require("biomaRt")
human = useEnsembl(biomart = "genes", dataset = "hsapiens_gene_ensembl")
mouse = useEnsembl(biomart = "genes", dataset = "mmusculus_gene_ensembl")
genesV2 = getLDS(attributes = c("mgi_symbol"), filters = "mgi_symbol", values = x , mart = mouse, attributesL = c("hgnc_symbol"), martL = human, uniqueRows=T)
humanx <- unique(genesV2[, 2])
mouse_genes_number <- length(x)
human_genes_number <- length(humanx)
if(mouse_genes_number != human_genes_number){
genes_not_trans <- setdiff(x, genesV2$MGI.symbol)
print("These genes could not be translated:")
print(genes_not_trans)
print(paste("A total number of ",length(genes_not_trans),"genes could not be translated!"),sep=" ")
}else{
print("All genes were translated successfully!")
}
return(humanx)
}
ConvertedGenes <- convertMousetohuman(musGenes)
Indeed, the function must return something, if only a NA. Otherwise, one cannot use it to convert a list of gene symbols and append them to a data-frame or replace the initial list of human genes.