Genes can be referred to by their names, symbols, row numbers in the gene table, or a logical vector referring to the gene table rows. This function accepts all these possibilities and returns the row number in the gene table for the given genes,
Arguments
- data
The grandR object
- gene
A vector of genes. Can be either numeric indices, gene names, gene symbols or a logical vector
- regex
Treat gene as a regex and return all that match
- remove.missing
if TRUE, do not return missing genes (return NA otherwise)
- warn
if TRUE emit a warning if not all genes are found
Examples
sars <- ReadGRAND(system.file("extdata", "sars.tsv.gz", package = "grandR"),
design=c("Cell",Design$dur.4sU,Design$Replicate))
#> Warning: Duplicate gene symbols (n=1, e.g. MATR3) present, making unique!
ToIndex(sars,c("MYC"))
#> MYC
#> 436
ToIndex(sars,GeneInfo(sars)$Symbol=="MYC")
#> [1] 436