##Multi Omic Oscillations Patterns
The procedure requires to download all the files and run the script MOOsEX.R, all functions are gathered in MOOsFun.R
The data are represented in lists saved in R data format, also all the considered pathways and metabolic pathways.
All the data are disposed in order as they are listed in the supplementary material and are referred to the organism Escherichia coli K-12 MG1655, KEGG identifier: "eco".
These data are calculated with the algorithm NBA and are related to the interactome's weights of the metabolic pathways.
osc.list.w.in.Rdata
osc.list.w.out.Rdata
These data are referred to the binary matrices. that for each metabolic network the operons ( at a genomic level ) and protein complexes (poly) (at the proteomic level) describe their presence.
osc.eco.poly.ms.Rdata
osc.eco.operon.ms.Rdata
This is a list of pathways where for each one is associated the CAI, protein abundances, gene sequences, gene symbols, protein names, gene lengths and the genes' 5'-3' (+) or 3'-5' (-) .
osc.paths.list.Rdata
For each pathway considered are present all the possible SOPs and MOPs discretised.
Operons AND protein complexes compressions
osc.paths.list.cai.poly.Rdata #SOPs of CAI
osc.paths.list.pa.poly.Rdata #SOPs of Protein Abundance
osc.paths.list.caipa.poly.Rdata #MOPs of CAI and Protein Abundance
Operons Compressions
osc.paths.list.pa.operons.Rdata #SOPs of CAI
osc.paths.list.cai.operons.Rdata #SOPs of CAI
osc.paths.list.caipa.operons.Rdata #SOPs of CAI
For each pathway considered are present all the PFs as is described in the paper.
osc.paths.list.suzukietall.Rdata #Suzuki et All.
osc.paths.list.norfloxacin.Rdata #Faith et All.
##Oscillatory patterns identification In the folder score of omic patterns - toy examples are present some tests with all the possible combinations of 3,4,5 discretisation levels of patterns of length 9. As described in the paper is computed: P_u (labelled prob in these files), the oscillation score (labelled score) and its normalisation (nrm.sc).
The pseudo-code of the Algorithm 1 is described in the paper.
A small example of the Algorithm 1 is linked here: https://github.com/lodeguns/NetBasAdj and in integrated in this source code.
##R Session Info
Please note that the software and the packages linked are built on R version 3.2.5 (2016-04-14)
Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows >= 8 x64 (build 9200)
locale:
LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United Kingdom.1252
LC_MONETARY=English_United Kingdom.1252 LC_NUMERIC=C
LC_TIME=English_United Kingdom.1252
attached base packages:
stats graphics grDevices utils datasets methods base
other attached packages:
d3heatmap_0.6.1.1 cluster_2.0.4 PST_0.88 RColorBrewer_1.1-2 TraMineR_1.8-11.1 KernSmooth_2.23-15 classInt_0.1-23
loaded via a namespace (and not attached):
Rcpp_0.12.5 DEoptimR_1.0-4 plyr_1.8.3 prabclus_2.2-6 base64enc_0.1-3
class_7.3-14 tools_3.2.5 mclust_5.2 boot_1.3-18 rpart_4.1-10
dendextend_1.2.0 digest_0.6.9 jsonlite_0.9.22 gtable_0.2.0 lattice_0.20-33
png_0.1-7 Matrix_1.2-6 yaml_2.1.13 mvtnorm_1.0-5 gridExtra_2.2.1
e1071_1.6-7 trimcluster_0.1-2 fpc_2.1-10 htmlwidgets_0.6 diptest_0.75-7
stats4_3.2.5 grid_3.2.5 nnet_7.3-12 robustbase_0.92-6 data.table_1.9.6
flexmix_2.3-13 survival_2.39-4 foreign_0.8-66 latticeExtra_0.6-28 Formula_1.2-1
kernlab_0.9-24 whisker_0.3-2 ggplot2_2.1.0 magrittr_1.5 modeltools_0.2-21
MASS_7.3-45 Hmisc_3.17-4 scales_0.4.0 htmltools_0.3.5 splines_3.2.5
colorspace_1.2-6 acepack_1.3-3.3 munsell_0.4.3 chron_2.3-47