rename_genes {dnapath}

Rename genes in the differential network analysis

Description

Rename genes in the differential network analysis

Usage

rename_genes(x, gene_mat = NULL, to = NULL, species = NULL, ...)

Arguments

x

A 'dnapath_list' or 'dnapath' object from dnapath, a pathway list, or a vector of gene names.

gene_mat

(Optional) A matrix of key value pairs. The first column should contain current gene names, and the second column the new names. Any genes that are not in this matrix will retain their current names. This can be any user-defined mapping, or the mapping obtained using entrez_to_symbol or symbol_to_entrez.

to

(Optional) Setting to = "symbol" will rename entrezgene IDs to gene symbols; this will automatically call the entrez_to_symbol() function to obtain the mapping for gene_mat. The species argument must also be specified when to is used.

species

(Optional) Must be specified when setting to = "symbol". This argument is passed into entrez_to_symbol.

...

Additional arugments are passed into entrez_to_symbol in the case that to and species are specified. This may be useful to specify the dir_save argument to save the mapping obtained from biomaRt for offline use.

Value

Returns x with all gene names updated according to gene_mat.

Note

Internet connection is required to connect to use entrez_to_symbol or symbol_to_entrez.

See Also

entrez_to_symbol, symbol_to_entrez

Examples

data(meso)
data(p53_pathways)
set.seed(0)
results <- dnapath(x = meso$gene_expression, pathway_list = p53_pathways,
                   group_labels = meso$groups, n_perm = 10)
summary(results[[1]])  # Summary of pathway 1; note that it uses entrezgene IDs.


# Rename the entrezgene IDs into gene symbols.
results_sym <- rename_genes(results, to = "symbol", species = "human")
summary(results_sym[[1]]) # Now the summary uses gene symbols.