Some examples of CALANGO output are available under
docs/articles/results in the CALANGO Github
repository, and their output pages are linked below.
- Example 1 relates to the case study “Homologous regions and biological roles associated with prophage density in pathogenic and free-living Escherichia coli”.
- Example 2 relates to the case study Homologous regions associated with maximum height in Angiosperms.
Both examples are presented as part of the manuscript CALANGO: a phylogeny-aware comparative genomics tool for discovering quantitative genotype-phenotype associations across species. Please navigate to one of the links below to check the examples:
- Example1-domain2GO-count
- Example1-domain2GO-count-less-phages
- Example1-domain2GO-freq
- Example1-domain2Pfam-count
- Example1-domain2Pfam-count-less-phages
- Example1-domain2Pfam-freq
- Example2-Pfam-count
- Example2-Pfam-freq
These examples can be independently reproduced by running the script
below. After running CALANGO::retrieve_data_files(), the
main input files (which can be used as templates for other studies) will
be located under subfolder /parameters.
install.packages("CALANGO")
library(CALANGO)
# Change target.dir to save under a different folder if needed
target.dir <- "data"
# Change to increase number of cores.
ncores <- 1
CALANGO::retrieve_data_files(target.dir)
# Get CALANGO input files for the examples
inputfiles <- dir(paste0(target.dir, "/parameters"), full.names = TRUE)
# run for all example files
for (i in seq_along(inputfiles)){
cat("\nProcessing example", i, "of", length(inputfiles), "\n")
defs <- CALANGO::run_CALANGO(inputfiles[i], cores = ncores)
}