| gene_indexer {ccRemover} | R Documentation |
Determines which of the genes contained in the dataset are annotated ti the cell-cycle. This is a preprocessing function for ccRemover. Genes can be either mouse or human and either official gene symbols, Ensembl, Entrez or Unigene IDs.
gene_indexer(gene_names, species = NULL, name_type = NULL)
gene_names |
A vector containing the gene names for the dataset. |
species |
The species which the gene names are from. Either
|
name_type |
The type of gene name considered either, Ensembl gene IDS
( |
A vector containg the indices of genes which are annotated to the cell-cycle
set.seed(10) # Load in example data data(t.cell_data) head(t.cell_data[,1:5]) # Center example data t_cell_data_cen <- t(scale(t(t.cell_data), center=TRUE, scale=FALSE)) # Extract gene names gene_names <- rownames(t_cell_data_cen) # Determine which genes are annotated to the cell-cycle cell_cycle_gene_indices <- gene_indexer(gene_names = gene_names, species = "mouse", name_type = "symbol") # Create "if_cc" vector if_cc <- rep(FALSE,nrow(t_cell_data_cen)) if_cc[cell_cycle_gene_indices] <- TRUE # Can allow the function to automatically detect the name type cell_cycle_gene_indices <- gene_indexer(gene_names = gene_names, species = NULL, name_type = NULL)