Distance measures of the the original and jackknifed random modules
Source:R/data.R
random_dist_jk.RdDistance measures per replicate pair for the original and all jackknifed versions of the random modules.
Format
A named list with 232 elements containing the distance measures per (original or jackknifed) module version. Each element is a data frame with 72 rows and 10 columns:
- 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).
- 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').
- gene_removed
Character, the name of the gene removed by jackknifing (NA in case of module type 'orig').
- replicate1, replicate2
Character the names of the replicates compared.
- species1, species2
Character, the names of the species
replicate1andreplicate2belong to, respectively.- dist
Numeric, distance measure ranging from 0 to 1, calculated based on the correlation of intramodular connectivities.
Details
The jackknifed versions of the modules were created by removing each target gene assigned to a module (the regulators were never excluded). The distance measures were calculated based on the correlation of intramodular connectivities: $$dist = \frac{1 - cor.kIM}{2}$$ (a correlation of 1 corresponds to a distance of 0, whereas a correlation of -1 corresponds to a distance of 1). Each element of the list corresponds a jackknife module version and contains the distance measures between all possible pairs of replicates for this module version.