Preparing Inputs

Here we store the scripts used to build the PHONEMeS inputs for the data analysis. These inputs are generated simply by running the R scripts prepareGMM_FC_UACC257_redundant_sites.R and prepareGMM_FC_A2058_redundant_sites.R for each cell-line respecitvely.

Steps to build the inputs

Below we describe the main steps followed to build the PHONEMeS inputs.

• We read the Mass-Spect data inst/Endothelin _ShortTerm_UACC257_new180822_SiteLevel.csv and inst/Endothelin _ShortTerm_A2058_new_180822_SiteLevel.csv containing the site level information (fold changes and significance as described in the paper).
• We log2 transform the fold changes.
• We assign a threshold value threshQ=0.1 to the differential abundance.
• Based on the data tables (inst/Endothelin _ShortTerm_UACC257_new180822_SiteLevel.csv & Endothelin _ShortTerm_A2058_new180822_SiteLevel.csv), we generate the GMM objects containing a list of matrices for each site. Each matrix contains different values and labels assigned to each measurement at all time-points as below:
• The Indiv columns contain the scores we assign to each of the measurements by computing the log2 value of the ratio between the significance of a measurement at a specific time-point (as found in the data tables) over the threshQ value. Sites with a qValue < threshQ on a specific time-point will be assigned a negative score, otherwise they will be assigned a positive score.
• The clus columns contain information about significance status of the measurement. If qValue < threshQ, then to the data-point it will be assigned a Perturbation P status, otherwise the measurement will take a Control C status.
• The FCvCaPval contain the q significance values for each measurement.
• The status columns show whether a measurement has been observed to be higly regulated (OK) or not (FP). A site with a fold change higher than 1.5 is considered to be as highly regulated.
• The FCvC column contains the log2 fold changes of EDN activated sites compared to control.

Generating and storing the inputs

We build two separate data objects dataGMM_UACC257.RData and dataGMM_A2058.RData and we keep them stored on the local directory.