#This is a sample parameter file for KOMODO2. Most variables are self-explanatory, and a formal definition of each can be found in KOMODO2 documentation.
KOMODO2 <- list(annotation_files_dir = "../../data/gene2GO/", #Directory where annotation files are located. If not provided, file described in variable "dataset.info" should contain absolute paths to annotation files
output.dir = "../../results/GO_Pan_proxy_2/", #output directory for results
dataset.info = "../../data/metadata/GO_metadata_Pan_proxy.txt", #genome metadata file, it should contain at least, for each genome: 1) path for annotation data; 2) phenotype data (numeric); 3) normalization data (numeric)
x.column = 2, #which column contains phenotype data?
ontology = "GO", #which dictionary data type?
dict.path = "", #file for dictionary file (two-column file containing annotation IDs and their descriptions, not needed for GO
column = "GO", #which column in annotation file should be used (column name)
denominator.column = "", #which column contains normalization data (numeric)
tree_path = "../../data/trees/tree_genome_IDs.nwk", #path for tree file
tree_type = "newick", #tree file type (either "nexus" or "newick", case-sensitive)
cores = 4, #how many cores to use?
#ADVANCED PARAMETERS (not really...)
#These parameters are basically to tell KOMODO2 how much graphical output it should produce. We configure it to generate plots only for annotation terms with corrected q-values for phylogenetically independent contrasts smaller than 0.5.
linear_model_cutoff = 0.5
)
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