run_KOMODO2: Run the KOMODO2 pipeline

In fcampelo/KOMODO2-CRAN: Kegg Orthology EnrichMent Online DetectiOn

Description

This script runs the complete LCFD workflow of KOMODO2 and generates the HTML5 output pages and export files.

Usage

run_KOMODO2(defs, cores = NULL)

Arguments

defs	either a KOMODO2-type list object or a path to a text file containing the required definitions (see Details).
cores	positive integer, how many CPU cores to use (multicore acceleration does not work in Windows systems). Setting this parameter overrides any 'cores' field from 'defs'. Multicore support is currently implemented using the 'parallel' package, which uses forking (which means that multicore support is not available under Windows)

Details

The script expects a 'KOMODO2'-type list, which is a list object containing _at least_ the following fields:

• test.path (char string): path to the folder containing annotation files of the test group

• back.path (char string): path to the folder containing annotation files of the background group

• x.path (char string): path to the file containing the genomes' attributes (for correlation test)

• y.path (char string): path to the folder containing the the genomes and their annotations (for correlation test)

• ontology (char string): which ontology to use. Currently accepts "GO" or "Gene Ontology", "KEGG" and "other".

• dict.path (char string): file with the dictionary (terms and their meaning) of the ontology, if 'ontology' is set as "other".

• type (char string): comparison module to use. Currently only the "correlation" type is implemented.

The input definitions can also be passed as a file path. If that is the case the file must be a text file with a 'field = value' format. Blank likes and lines starting with '#' are ignored. Required fields are the same described for the 'KOMODO2' list described above.

Examples

## Not run: 
# Build an input list:

fpath1 <- system.file("extdata", "gene2GO", package="KOMODO2")
fpath2 <- system.file("extdata", "metadata/GO_metadata_Pan_proxy.txt", package="KOMODO2")
fpath3 <- system.file("extdata", "trees/tree_genome_IDs.nwk", package="KOMODO2")

defs <- list(annotation_files_dir = fpath1,
             output_dir = "./results/GO_Pan_proxy/",
             dataset.info = fpath2,
             x.column = 2,
             ontology = "GO",
             dict.path = "",
             column = "GO",
             denominator.column = "",
             tree_path = fpath3,
             tree_type = "newick",
             linear_model_cutoff = 0.5,
             type = "correlation")

# output <- run_KOMODO2(defs, cores = 3)

## End(Not run)

fcampelo/KOMODO2-CRAN documentation built on March 7, 2020, 6:35 a.m.