hyp_to_table {hypeR}R Documentation

Export hyper dataframe to table

Description

Export hyper dataframe to table

Usage

hyp_to_table(df, file.path, sep = "\t", cols = seq_len(ncol(df)))

Arguments

df

A hyper dataframe

file.path

Output file path

sep

The field separator string

cols

Dataframe columns to include

Value

None

Examples

# 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")
[Package hypeR version 1.00.0 Index]