every element in the result matrix of running Prune() is zero.

[min0609]

Hi, First of all, thank you for this wonderful tool. I’m wondering why every element in the result matrix of running Prune() is zero. I show you the code i ran.

data(motifAnnotations_hgnc) motifRankings <- importRankings("./hg38refseq-r8010kb_up_and_down_tss.mc9nr.feather") gene <- colnames(motifRankings)

ac_ntf <- read.table("co_fc.txt") ac_tf <- read.table("co_tf_fc.txt") gene_ntf <- read.csv("gene_ntf.csv") gene_tf <- read.csv("gene_tf.csv")

coexpressed <- Merge(ac_ntf,ac_tf,gene_ntf,gene_tf,gene) O <- Screen(coexpressed) copaired <- Copaired(O) genesets <- Genesets(copaired) genesets_list <- levels(as.factor(copaired$V1))

Regulons <- Prune(O, genesets, genesets_list, motifRankings, motifAnnotations_hgnc) copaired2 <- Copaired2(Regulons) genesets2 <- Genesets(copaired2)

The ‘O’, result of the function Screen, has elements of 1 or 0, but I got a matrix with all zero elements from the function Prune(). For this reason, the function Copaired2 gives me no result. May I ask you why this is happening? Thank you very much in advance!

[Tonitrus2020]

The core of the Prune function is the cisTarget function from the RcisTarget package. The codes above seem correct but I'm not sure why the function returns to a blank matrix. My suggestions are as following: 1) Check the outlier matrix 'O', if it is in correct format; 2) Conduct the cisTarget function with your data along instead of using Prune function and see if it has correct output; 3) If it can generate right output, the problem may caused by package version or something and you can try reinstall the RcisTarget pacakage; if it cannot generate right output, the problem may come from your data, or the choice of gene-motif rankings.

[ghost]

I am having the same issue in the python version. It's all zeros. I am trying to understand why.

[ghost]

i think what could help is if you were to provide a little input file as an example that is runnable so we can understand whether we have the input format data correct or not. could be a start

[Tonitrus2020]

Maybe you guys can send a small part of your outlier matrix to us and the email address is yuyz16@mails.tsinghua.edu.cn and we can find what caused the unexpected results. As far as we know, this may be caused by the input format of the outlier matrix, or more specifically, the name of the genes in capitalized form or not. But there could also be other reasons and we can only find them after we obtain the outlier matrix.