hyp_to_table {hypeR} | R Documentation |
Export hyper dataframe to table
hyp_to_table(df, file.path, sep = "\t", cols = seq_len(ncol(df)))
df |
A hyper dataframe |
file.path |
Output file path |
sep |
The field separator string |
cols |
Dataframe columns to include |
None
# Grab a list of curated gene sets REACTOME <- ex_get("C2.CP.REACTOME") # Genes involed in tricarboxylic acid cycle symbols <- c("IDH3B","DLST","PCK2","CS","PDHB","PCK1","PDHA1","LOC642502", "PDHA2","LOC283398","FH","SDHD","OGDH","SDHB","IDH3A","SDHC", "IDH2","IDH1","OGDHL","PC","SDHA","SUCLG1","SUCLA2","SUCLG2") # Perform hyper enrichment hyp <- hypeR(symbols, REACTOME, bg=2522, fdr=0.05) # Export hyp_to_table(hyp, file.path="pathways.txt")