Tool: pathfindR - Enrichment Analysis using Active Subnetworks
16
gravatar for egeulgen
2.5 years ago by
egeulgen990
Istanbul
egeulgen990 wrote:

Hello all,

I would like to introduce our group's active-subnetwork-oriented enrichment R package: pathfindR (latest release is v1.5.1).

This tool is designed to improve enrichment analysis by firstly identifying active subnetworks in differential expression/methylation data using a protein-protein interaction network. It then performs enrichment analysis (Over-Representation Analysis). By utilizing the interaction information, pathfindR identifies most of the key involved processes.

  • pathfindR provides the human gene sets KEGG, Reactome, BioCarta, GO-MF, GO-BP, GO-CC and GO-All (BP+MF+CC) and the M.musculus KEGG mmu_KEGG gene set for enrichment analysis. The user can also use any other custom gene sets.
  • pathfindR also creates pathway diagrams for hsa-KEGG with the involved genes colored by change values or visualizations of interactions of genes involved in the pathways and interaction graphs for other gene sets, displaying the interactions of involved genes
  • The package allows for clustering of enriched terms and establishment of representative terms. This allows for further abstraction and reduces the complexity of analysis. The available clustering approaches are hierarchical and fuzzy.
  • pathfindR provides functionality to score terms for individual samples and plot a heat map of the scores. This allows the user to investigate how a gene set is altered in a given sample (or in cases vs. controls).
  • pathfindR provides functionality to combine and compare 2 pathfindR enrichment results
  • the package also offers numerous visualization options, including term-gene interaction graph, term-gene interaction heatmap, UpSet plots and graphs of identified subnetworks.

You can install the released version of pathfindR from CRAN via:

install.packages("pathfindR")

And the development version from GitHub via:

install.packages("devtools") # if you have not installed this
devtools::install_github("egeulgen/pathfindR")

You can read more about the method, its example applications on 3 different datasets and comparison with other available methods in our 2019 article.

Find out more in the pathfindR website and check out the pathfindR tutorial.

ADD COMMENTlink modified 1 day ago • written 2.5 years ago by egeulgen990
4

It's useful.
1. Why not to bioconductor, containing lots of bioinformatics R packages instead of CRAN?
2. no examples of pathmap in the vignette.
3. An enhancement: Visualise the results of run_pathfindR, besides the table show.

Thank you.

ADD REPLYlink modified 2.3 years ago by zx87549.6k • written 2.4 years ago by Zhilong Jia1.6k
1

Thank you for the feedback! To answer them:

  1. We did not think it would make any difference
  2. We will try to include an example for pathmap in the next version
  3. The pathways are already visualized and can be viewed through the HTML reports. Would you expand on how we could provide more visualizations?

Thanks again,

-E

ADD REPLYlink modified 2.3 years ago • written 2.3 years ago by egeulgen990
  1. Precision advertising. The targeting users of pathfindR are bioinformaticians, which are the users of Bioconductor, while the users of CRAN is R users. Getting more chance to encounter target audiences of pathfindR via Bioconductor. Anyway, not a problem.
  2. I did not check the HTML report as I cannot run the examples after installing pathfindR and filed an issue at Github. I mean the pathway enrichment itself, not visualization for each pathway based on pathview.
ADD REPLYlink written 2.3 years ago by Zhilong Jia1.6k

We’re looking into your issue on Github. We will try to include a visualization of the enrichment results in the next version (considering a bubble chart but feel free to share any ideas of what you had in mind).

ADD REPLYlink modified 2.3 years ago • written 2.3 years ago by egeulgen990

I will second the idea of a bubble chart. This is one of the easier/better GO packages to use that I've tried, but it lacks the visualization options of some others. Keep up the good work.

ADD REPLYlink written 2.1 years ago by jared.andrews077.0k

Can you please give a tutorial by taking some examples of a gene.

ADD REPLYlink modified 2.5 years ago • written 2.5 years ago by kalyanimeha30
2

You can see an example application in the vignette (browseVignettes("pathfindr_vignette")). We also have a wiki.

ADD REPLYlink modified 2.3 years ago • written 2.5 years ago by egeulgen990

HI This is a great package. I'm having a little trouble with the pathway scoring part of the tutorial. I'm not sure how to create the RA_exp_mat for my data?

thanks again

ADD REPLYlink written 2.1 years ago by amgodogma0

The expression matrix for the pathway scores is the same matrix as the one you use for differential expression analysis. Columns are samples, rows are genes and the values are expression values.

ADD REPLYlink written 2.1 years ago by egeulgen990

Hi the package seems to be exactly what I need but I have an issue in install it, I try with the pak command: pak::pkg_install("pathfindR") It gives me always this error: Error: callr subprocess failed: Failed to download class from https://cran.rediris.es//bin/macosx/el-capitan/contrib/3.6/class_7.3-17.tgz. Failed to download cluster from https://cran.rediris.es//bin/macosx/el-capitan/contrib/3.6/cluster_2.1.0.tgz. Failed to download codetools from https://cran.rediris.es//bin/macosx/el-capitan/contrib/3.6/codetools_0.2-16.tgz. Failed to download DEoptimR from https://cran.rediris.es//bin/macosx/el-capitan/contrib/3.6/DEoptimR_1.0-8.tgz. Failed to download diptest from https://cran.rediris.es//bin/macosx/el-capitan/contrib/3.6/diptest_0.75-7.tgz. Failed to download doParallel from https://cran.rediris.es//bin/macosx/el-capitan/contrib/3.6/doParallel_1.0.15.tgz. Failed to download flexmix from https://cran.rediris.es//bin/macosx/el-capitan/contrib/3.6/flexmix_2.3-15.tgz. Failed to download foreach from https://cran.rediris.es//bin/macosx/el-capitan/contrib/3.6/foreach_1.5.0.tgz. Failed to download fpc from `https://cran.rediris.es//bin/

I am using R 3.6.3, in a mac Os x Catallina. May it be a Catalina-related problem?

Thanks

ADD REPLYlink written 3 months ago by andrea.curtabbi0

Anything wrong with the recommended install.packages("pathfindR")?

ADD REPLYlink written 3 months ago by ATpoint38k

hey, I think it's an issue with pak. install.packages("pathfindR") should work. You may try with devtools for the development version:

install.packages("devtools") # if you have not installed "devtools"
devtools::install_github("egeulgen/pathfindR")
ADD REPLYlink written 3 months ago by egeulgen990

Hi there! I have tried both pak::pkg_install("egeulgen/pathfindR") and devtools::install_github("egeulgen/pathfindR"), both didn't work:

With pak::pkg_install("egeulgen/pathfindR"), I get the following error:

Error: callr subprocess failed: Failed to download DBI from https://cran.rstudio.com//bin/windows/contrib/3.6/DBI_1.1.0.zip. Failed to download DEoptimR from https://cran.rstudio.com//bin/windows/contrib/3.6/DEoptimR_1.0-8.zip. Failed to download MASS from https://cran.rstudio.com//bin/windows/contrib/3.6/MASS_7.3-51.6.zip. Failed to download Matrix from https://cran.rstudio.com//bin/windows/contrib/3.6/Matrix_1.2-18.zip. Failed to download R.methodsS3 from https://cran.rstudio.com//bin/windows/contrib/3.6/R.methodsS3_1.8.0.zip. Failed to download R.oo from https://cran.rstudio.com//bin/windows/contrib/3.6/R.oo_1.23.0.zip. Failed to download R.utils from https://cran.rstudio.com//bin/windows/contrib/3.6/R.utils_2.9.2.zip. Failed to download RCurl from https://cran.rstudio.com//bin/windows/contrib/3.6/RCurl_1.98-1.2.zip. Failed to download RSQLite from https://cran.rstudio.com//bin/windows/contrib/3.6/RSQLite_2.2.0.zip. Failed to download XML from `https://cran.rstudi

And with devtools::install_github("egeulgen/pathfindR"), I get the following error:

Skipping 1 packages not available: pathfindR.data Installing 35 packages: pathfindR.data, org.Hs.eg.db, backports, generics, tidyselect, tweenr, polyclip, RcppEigen, dplyr, tidyr, RcppArmadillo, modeltools, mclust, DEoptimR, R.methodsS3, jsonlite, openssl, XVector, zlibbioc, bitops, tinytex, ggforce, ggrepel, tidygraph, graphlayouts, flexmix, prabclus, diptest, robustbase, kernlab, R.oo, Biostrings, XML, graph, RCurl Installing packages into ‘C:/Users/manojka/Documents/R/win-library/3.6’ (as ‘lib’ is unspecified) Error: Failed to install 'pathfindR' from GitHub: (converted from warning) package ‘pathfindR.data’ is not available (for R version 3.6.2)

Is there anyway around this? Thanks!

ADD REPLYlink written 12 weeks ago by manojkamalanathan7110

hey,

package ‘pathfindR.data’ is not available (for R version 3.6.2)

You need to have R version 4 installed.

ADD REPLYlink written 11 weeks ago by egeulgen990

Thanks you, that works!

ADD REPLYlink written 11 weeks ago by manojkamalanathan7110

What a great package! Thanks!

ADD REPLYlink written 9 weeks ago by jungjoon.kim0
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