read_eggnog_mapper: Function for reading in eggnog-mapper annotations and...

In leylabmpi/LeyLabRMisc: Ley Lab misc R functions, rmd templates, etc.

Function for reading in eggnog-mapper annotations and returning tidy subsets of the info

Description

Many of the data in the eggnog-mapper annotation table (eg., generated by the LLG pipeline) is encoded as comma-delimited lists within a single column (eg., KEGG pathways). This makes it challenging to "tidy" the table.

Usage

read_eggnog_mapper(
  infile = NULL,
  cmd = NULL,
  sep = "\t",
  nrows = Inf,
  to_keep = c("COG", "KEGG pathway", "CAZy"),
  column_names = c("query_name", "seed_eggNOG_ortholog", "seed_ortholog_evalue",
    "seed_ortholog_score", "Predicted_taxonomic_group", "Predicted_protein_name",
    "Gene_Ontology_terms", "EC_number", "KEGG_ko", "KEGG_Pathway", "KEGG_Module",
    "KEGG_Reaction", "KEGG_rclass", "BRITE", "KEGG_TC", "CAZy", "BiGG_Reaction",
    "tax_scope__eggNOG_taxonomic_level_used_for_annotation", "eggNOG_OGs", "bestOG",
    "COG_Functional_Category", "eggNOG_free_text_description")
)

Arguments

infile	Path to eggnog-annotation table file
cmd	command instead of input file (eg., "gunzip -c INFILE")
sep	table value delimiter
nrows	Number of table rows to read. If Inf, all lines will be read.
to_keep	Which functional grouping to keep (eg., KEGG pathways)?
column_names	The column names to use for the table (use NULL if the input table has column names)

Details

This function will read in the table and output a tidy table of one part of the table (eg., COG functional categories or KEGG pathways).

The function will also provide info on how to obtain metadata for function groupings.

Value

data.table

leylabmpi/LeyLabRMisc documentation built on Nov. 3, 2022, 3:45 p.m.