ToIndex: Obtain the indices of the given genes

In grandR: Comprehensive Analysis of Nucleotide Conversion Sequencing Data

Obtain the indices of the given genes

Description

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,

Usage

ToIndex(data, gene, regex = FALSE, remove.missing = TRUE, warn = TRUE)

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

Value

Numeric indices corresponding to the given genes

See Also

GeneInfo

Examples

sars <- ReadGRAND(system.file("extdata", "sars.tsv.gz", package = "grandR"),
                  design=c("Cell",Design$dur.4sU,Design$Replicate))
ToIndex(sars,c("MYC"))
ToIndex(sars,GeneInfo(sars)$Symbol=="MYC")

grandR documentation built on April 4, 2025, 2:27 a.m.