reimandlab/activepathways

Integrative pathway enrichment analysis of multivariate omics data

activepathways's Issues

rows were removed from scores because they are not found in the background

Hi,

I am using the ActivePathways tool, but I am encountering an issue

2861 rows were removed from scores because they are not found in the background
I believe there might be an underlying problem here, but I haven't been able to figure it out.

Here is my scores matrix:

ATAC-Seq RNA-Seq
A0A024R962 1.000000000 0
P08603 1.000000000 0
A0A0D9SG88 1.000000000 0
C9JPG5 0.001133218 1
Q59G50 0.001133218 1
Q13275 0.001133218 1

My matrix has Uniprot ID but I also tried with entrez ID and HGNC symbols. But the result is the same. I could not understand the problem but the number of the rows seemed a bit odd to me.

update vignettes and documentation

TCGA analysis

Hi, this package and article was based on the analysis on PCAWG datasets. May I apply it to WES datasets ftom TCGA open access data? Thank you very much!

ERROR (test_merge_p_values.r:43:5): Merged p-values are correct

Hi,
Thanks for using and importing data.table.
In reverse dependency testing of the next data.table release, I'm running R CMD check for ActivePathways and seeing the following error. It's the same one currently occurring on CRAN just on r-oldrel-macos, oddly.
https://www.r-project.org/nosvn/R.check/r-oldrel-macos-x86_64/ActivePathways-00check.html
And here's my output: 00check.log
Would installing the Suggested package EmpiricalBrownsMethod make this test pass, perhaps?
Thanks, Matt

add example dataset to README.rd

miRNA results

Hi, I want to know if the differential miRNA results are applicable to DPM.

vignette compilation fails

outdated parameter name remains in vignette (cytoscape.filenames vs cytoscape.file.dir)

ActivePathways results visualization

Hi,
First, thank you for your work on this very useful tool! I did not have any issue to run your function.
However, I don't really get how you obtained the Nat Commun paper figures with the nodes represented with pie charts showing the contribution of each dataset in the enrichment results. I used Cytoscape EnrichmenMap and load my ActivePathways output folder (with legend.pdf, pathways.txt, pathways.gmt and subgroups.txt files) and I can see the network in the EnrichmenMap view but I can't find the way to get the pie chart in the node with the contribution of each dataset I used. By default, it assumes that my first dataset is "pathways" and my second one is "subgroups". How can I change that?

Many thanks in advance for your help!
Best,
Lise

pval correction of ranked hypergeometric tests

Hi all,
First, thank you for keeping this repository very interactive, I really appreciate it.
I had a question on the method itself this time. If I understand well, for each pathway, your method sets a sub-list of genes from the pathway gene set to perform successive ranked hypergeometric tests. I understand that it selects the minimal p-value from these tests to get the Ppathway metric which is, afterwards, corrected for multiple testing (to take into account the fact that there are k tests for k pathways in the database) and it gets Qpathway. What you called ranked hypergeometric test is also known as mHG test (minimum hypergeometric test) for which the resulting p-values are always corrected afterwards. Thus, I have the feeling that, even if you performed a correction on Ppathway, the damage has already been done since a correction would be necessary just after generating the mHG p-values and so before the identification of Ppathway and its correction for multiple testing. I guess it would not change the choice of the p-value representing Ppathway but it would change its value and so the final value of Qpathway which is the one used to identified enriched pathways. Did I miss something? What is the rationale behind your choice?

Thank you so much for your help,
Best,
Lise

package naming conflict

ActivePathways vs activePathways

Package archived from CRAN

Hi,
Thank you for your package. I use it a lot. I've noticed it was archived from CRAN. Is there a relevant reason for the archive?
Thank you for all the hard work.
Kerem

How to create the tsv of p value?

Hi,
I want to use this package to analyze my snp data. But I have a problem to create the tsv of p value.
Could you give me some advice?
Thanks in advance.
Best wishes !
Liu

incomplete color legend with custom colors

When using a custom color palette for Cytoscape output, the color for the combined-only results does not show a label in the generated PDF. However, when not using a custom color palette, the label is shown as expected ("combined").

A minor note, "combined" could be replaced with something more informative and visible, such as "INTEGRATED-ONLY".

Output lists of gene definition

Hi again!
Thank you for your effort in this repository, it is well documented!! However, I may have a question about how I should extract the genes from the res R object (from res <- ActivePathways(scores, gmt.file, cytoscape.file.tag = "enrichmentMap__") ) for a given enriched pathway. I understand that they are listed in the Genes_X3UTR in the case where this pathway is enriched because of the X3UTR dataset but what about the "overlap" column? What is your definition of this list of genes?

Very sorry if you've already answered this question and I missed it,
Many thanks in advance for your assistance,
Best,
Lise

Issue with ActivePathways

Hi
I m not a bioinformatics person. I just followed what was written in the github. and I got this error. If there is a code for running the ActivePathways. Can you please share? [email protected]

I ran this code

dat <- as.matrix(read.table('C:/Users/praji/Documents/NSG vs Primary.txt.txt',fill= TRUE, header=TRUE, row.names= 1))
dat[is.na(dat)] <- 1
activePathways(dat, 'C:/Users/praji/Documents/NSGPrimary.gmt', return.all=TRUE,

•            cytoscape.file.dir="results")
  

Error in activePathways(dat, "C:/Users/praji/Documents/NSGPrimary.gmt", :
All values in scores must be in [0,1]

Error when additional arguments are not recognized

The latest update caused the function to not recognize the additional arguments. I've been using ActivePathways since it came out. and now when I try to run my code I get:

Error in ActivePathways(scores = as.matrix(pvals_table), gmt = gmt.file, :
unused arguments (geneset.filter = c(10, 500), cytoscape.file.tag = "Name")

Would be happy for your support.
Thank you for this great tool.
Kerem

CRAN package removed

ActivePathways removed from CRAN due to missing dependencies (metap)

Problem with gene set thresholds

I get the following error
('counts contains negative values. Something went very wrong.')
from hypergeometric test whenever I decrease the threshold of the geneset.filter = c(5, 1000) to c(3,1000)

Installation problem

Hi,

I'm having issues installing this package (See screenshot). Any ideas what I may be doing wrong?

Thanks!

create a method to export data as CSV