ID Conversion from Human Gene Symbols to Zebrafish Gene Symbols - r

Question

I am looking for an R solution (or a general logic solution) to convert Homo sapiens gene names into Danio rerio gene names. My current coding skills are fairly primitive, so I tried writing something with for-loops and if-statements, but it can only pick up one of the ortholog genes, however there are multiple. For example, for the human gene REG3G there are three zebrafish ortholog genes: si:ch211-125e6.13, zgc:172053, lectin. I have added the code I wrote, but that only picks up the last one, but I would like it to output all three.
I have also been having trouble finding R/BiomaRt code to help complete this task and would love any advice.
# Read excel file containing list of zebrafish genes and their human orthologs.
ortho_genes <- read_excel("/Users/talha/Desktop/Ortho_Gene_List.xlsx")
# Separate data from excel file into lists.
zebrafish <- ortho_genes$`Zebra Gene Name`
human <- ortho_genes$`Human Gene Name`
# Read sample list of differential expressed genes
sample_list <- c("GREB1L","SIN3B","NCAPG2","FAM50A","PSMD12","BPTF","SLF2","SMC5", "SMC6", "TMEM260","SSBP1","TCF12", "ANLN", "TFAM", "DDX3X","REG3G")
# Make a matrix with same number of columns as genes in the supplied list.
final_m <- matrix(nrow=length(sample_list),ncol=2)
# Iterate through every gene in the supplied list
for(x in 1:length(sample_list)){
# Iterate through every human gene
for(y in 1:length(human)){
# If the gene from the supplied list matches a human gene
if(sample_list[x] == human[y]){
# Fill our matrix in with the supplied gene and the zebrafish ortholog
# that matches up with the cell of the human gene
final_m[x,1] = sample_list[x]
final_m[x,2] = zebrafish[y]
}
}
}

Answer 1

You didn't specify the structure of ortho_genes. This is my guess:
ortho_genes <- tibble::tibble(Zebra = c("greb1l", "sin3b", "ncapg2", "fam50a", "psmd12", "bptf", "fam178a"),
Human = c("GREB1L","SIN3B","NCAPG2","FAM50A","PSMD12","BPTF","SLF2"))
You can simply index the table with sample_list (it's a vector, not a list)
sample_list <- c("NCAPG2", "SLF2", "GREB1L")
ortho_genes[ortho_genes$Human %in% sample_list,]
You also didn't specify how you want the output. Do you need a matrix? If you want to write the result into a file, a matrix may not be optimal.