reannotate_genes {easier} | R Documentation |
Performs gene re-annotation using curated data from the HGNC.
reannotate_genes(cur_genes)
cur_genes |
character string containing gene HGNC symbols to be consider for re-annotation. |
Source code adapted from quanTIseq helper function mapGenes from quantiseqr package.
A data.frame with the old gene HGNC symbol and the new corresponding gene HGNC symbol.
## Not run: # using a SummarizedExperiment object library(SummarizedExperiment) # Using example exemplary dataset (Mariathasan et al., Nature, 2018) # from easierData. Original processed data is available from # IMvigor210CoreBiologies package. library("easierData") dataset_mariathasan <- easierData::get_Mariathasan2018_PDL1_treatment() RNA_tpm <- assays(dataset_mariathasan)[["tpm"]] # Select a subset of patients to reduce vignette building time. pat_subset <- c( "SAM76a431ba6ce1", "SAMd3bd67996035", "SAMd3601288319e", "SAMba1a34b5a060", "SAM18a4dabbc557" ) RNA_tpm <- RNA_tpm[, colnames(RNA_tpm) %in% pat_subset] # Select some genes to check possible updated gene names genes_to_check <- rownames(RNA_tpm)[400:450] genes_info <- reannotate_genes(cur_genes = genes_to_check) ## End(Not run)