Reconstructs neighbor-joining trees based on pairwise distance measures between replicates.
Arguments
- dist_list
A named list containing the distance measures as data frames for all modules or jackknifed module versions, the output of
convertPresToDist. Required columns for the data frames:- regulator
Character, transcriptional regulator.
- module_size
Integer, the numer of target genes assigned to a regulator.
- type
Character, module type ("orig" = original or "jk" = jackknifed, only needed if the distances were calculated with jackknifing).
- id
Character, the unique ID of the module version (format: nameOfRegulator_jk_nameOfGeneRemoved in case of module type "jk" and nameOfRegulator_orig in case of module type "orig", only needed if the distances were calculated with jackknifing).
- gene_removed
Character, the name of the gene removed by jackknifing (NA in case of module type "orig", only needed if the distances were calculated with jackknifing).
- replicate1, replicate2
Character the names of the replicates compared.
- species1, species2
Character, the names of the species
replicate1andreplicate2belong to, respectively.- dist
Numeric, the distance measure to be used for the tree reconstruction.
- n_cores
Number of cores.
Value
A named list containing the neighbor-joining trees as phylo objects for all modules or jackknifed module versions in the input dist_list. All trees contain a component species that specifies which species each tip belongs to and a component info that stores metadata of the module/jackknifed module version in a data frame format.
Details
As part of the CroCoNet approach, pairwise module preservation scores are calculated between replicates, both within and across species, to quantify how similar module connectivity patterns are between the networks of two replicates (see calculatePresStats). These preservation scores are then converted into distance measures (see convertPresToDist).
This function first sorts the distance measures of each module/jackknifed module version into a distance matrix of all replicates, then based on this distance matrix reconstructs a tree using the neighbor-joining algorithm.
The procedure results in a single tree per module/jackknifed module version (depending on whether the preservation statistics were calculated with or without jackknifing, see see the parameter jackknife in the function calculatePresStats). The tips of the trees represent the replicates and the branch lengths represent the dissimilarity of module topology between the networks of 2 replicates. The trees are output as a list of phylo objects.
In the next steps of the pipeline, statistics based on these trees can be used to identify conserved and diverged modules and pinpoint target genes within these modules that contribute the most to conservation/divergence (see calculateTreeStats, fitTreeStatsLm, findConservedDivergedModules and findConservedDivergedTargets).