This script runs the complete LCFD workflow of KOMODO2 and generates the HTML5 output pages and export files.
either a KOMODO2-type list object or a path to a text file containing the required definitions (see Details).
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)
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.
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## 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)
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