R: Identifies genes annotated to the cell-cycle

gene_indexer {ccRemover} | R Documentation

## Identifies genes annotated to the cell-cycle

### Description

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.

### Usage

    gene_indexer(gene_names, species = NULL, name_type = NULL)

### Arguments

`gene_names` | A vector containing the gene names for the dataset.
`species` | The species which the gene names are from. Either `"human"` or `"mouse"`.
`name_type` | The type of gene name considered either, Ensembl gene IDS (`"ensembl"`), offical gene symbols (`symbol`), Entrez gene IDS (`"entrez"`), or Unigene IDS (`unigene`).

### Value

A vector containg the indices of genes which are annotated to the cell-cycle

### Examples

    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)

[Package ccRemover version 1.0.4 Index]