Below you will find pages that utilize the taxonomy term “causal edge”
Blog
Latest Progress on Network Inference and Edge Scoring
I have improved network inference part of the script slightly by changing the way of comparing intervention (presence of inhibitor and stimulus) and no intervention (presence of stimulus) data from in silico part.
Now, I’m using a function (simp) from an R package called StreamMetabolism, which gets time points and data values and (does integration) calculates the area under the curve (Sefick, 2009). I do this integration for both condition and then I compare them.
Blog
Scoring Edges Network Inference HPN-DREAM Challenge
Yesterday, I managed to infer a network for some part of in silico data from the challenge. Since the challenge also asks for scoring the edges in networks, I developed the script further and add a function for that.
edgeScorer function gets data object of average time points for each curve in intervention/no-intervention sets and scores each edge for each set of conditions. For this, first, it looks for the largest difference among the sets and set it as maxDifference and later, it stores differences divided by maxDifference in another data object.
Blog
Determining Edges More Progress on Network Inference
Lately, I have been writing an R script to infer network using in silico data. Last version of the script was reading MIDAS file and plotting expression profiles. I have modified it and now it reads MIDAS file, does some analyses and prints causal relations to a file. This file is a SIF file as required.
This dataset is generated with 20 antibodies but only 3 of them are perturbed. Also, for one, stimulus is missing.
Blog
Plotting Expression Profiles Data Analysis for Network Inference
For in silico data network inference I decided to develop a script because the existing tools have bugs and they are not compatible with the data. At the same time, I will try to report bugs and the compatibility issues to developers.
in silico data has 660 experiment results of 20 antibodies, 4 kinds of stimuli and 3 kinds of inhibitors. Antibodies are treated with a stimulus, say at t_0 and in the case of inhibitors, say at t_i, antibodies are pre-incubated for some time (t_pre) and then, treated with a stimulus.