nodeAttr: Writes node attributes for a network and data set

In saezlab/PHONEMeS-ILP: Building logic-based models from discovery high-content phosphoproteomics data

Writes node attributes for a network and data set

Description

This function writes node attributes and data tables for a data set matched to a network

Usage

nodeAttr(targets.On, nodesOF, drugsD, dataGMM, optParam, resFolder=getwd())

Arguments

targets.On	a list containing IDs of K/P perturbed in each condition
drugsD	a character vector that contains the drug treatments that we want the data for (they must match to row names of the data frames in the res(dataGMM) element)
nodesOF	a list of nodes perturbed or not in a set of conditions, as produced by nodesData
optParam	an OptParam object
resFolder	a character vector, the path to the folder where results will be written
dataGMM	a GMMres object, with at least the elements resFC and IDmap. resFC is a list resulting from the GMM, with a named element for each peptide (where the names map to the "dataID" column in IDmap(dataGMM), and inside each element a data matrix with named rows corresponding to drugs and named columns "clus", "status" and "FCvC", containing respectively the cluster from the GMM (P/C/I), the status (OK if p-value of fold change matches cluster assignment, FP if clus=P but p-val. not significant, FN if clus=C but p-val significant, I if clus=I), and the fold change vs control). IDmap is a data frame or matrix containing the map from site IDs to data IDs, with site IDs in a column named "S.cc" (mapping to nodesP), data ID in column named "dataID" (mapping to the names of resFC).

Value

This function writes NA and DA files

Author(s)

C. Terfve

saezlab/PHONEMeS-ILP documentation built on June 21, 2022, 5:36 p.m.