From b8d96f65784b321da3d2e1f01f0c26153b9db3f4 Mon Sep 17 00:00:00 2001 From: jschust <53572903+jschust@users.noreply.github.com> Date: Wed, 1 Jul 2020 11:40:05 -0400 Subject: [PATCH] Update README.md --- README.md | 20 ++++++++------------ 1 file changed, 8 insertions(+), 12 deletions(-) diff --git a/README.md b/README.md index cc285a9..a07cfe6 100644 --- a/README.md +++ b/README.md @@ -118,11 +118,11 @@ To view the summary information for a particular cluster or sample, enter "info * If more than one sample is contained within the input file (s), the dendrogam will be displayed. All output files generated by Proteinarium will be saved to the folder specified by the outputDirectory configuration option. By default, this goes to a folder called “Output” in the same directory as the Proteinarium.jar file. - **\\_ClusterAnalyses.csv:** cluster analysis files - **\\_Dendrogram.png:** dendrogram image - **\\_Dendrogram.txt:** representation of the dendrogram in Newick tree format - - + * **\\_ClusterAnalyses.csv:** cluster analysis files + * **\\_Dendrogram.png:** dendrogram image + * **\\_Dendrogram.txt:** representation of the dendrogram in Newick tree format + + ## 3. Viewing Clusters * When Proteinarium is done running, the GUI will navigate to a new window in which you can input the Cluster/Sample ID for which you are interesting in viewing or obtaining more information. @@ -133,14 +133,10 @@ To view the summary information for a particular cluster or sample, enter "info * If “View Cluster” is selected, the corresponding the output files will be available in the \/ folder. And the following files are generated: * **\\_Dendrogram.txt** - * For each of the five possible output networks--Group 1, Group 2, [Group 1 + Group 2], [Group 1 - Group 2], [Group 2 - Group 1], three files are generated to summarize that network. For example: - - 1. **\\_Group1_GeneSet.txt:** list of genes in the network and information about which input set they originated from (i.e. from Group 1, Group 2, or imputed from the interactome) and on how many samples the gene was found - - 2. **\\_Group1_Interactions.txt:** network interaction matrix - - 3. **\\_Group1.png:** image of the network + 1. **\\_Group1_GeneSet.txt:** list of genes in the network and information about which input set they originated from (i.e. from Group 1, Group 2, or imputed from the interactome) and on how many samples the gene was found + 2. **\\_Group1_Interactions.txt:** network interaction matrix + 3. **\\_Group1.png:** image of the network * If “Get Cluster Information” is selected, the following information will be appended to the file “SystemsOutput.txt” as indicated by the text box of the GUI. * *Average Distance (Height)*