Error in RegProcess Function: "arguments must have same length" When Processing ARACNe Network File

[ZGuofei]

Hello, I encountered an issue while using the PISCES pipeline for single-cell data analysis, specifically with the RegProcess function when processing an ARACNe-generated network file.

Here are the details:

Problem Description:

I am trying to process an ARACNe-generated network file using the RegProcess function. The network file is a TSV file generated from a gene expression matrix, containing three columns: Regulator, Target, and MI.
The expression matrix is a genes (rows) x samples (columns) matrix representing single-cell RNA-seq CPM-normalized data.
When I call the RegProcess function, I get the following error:

Error in tapply(1:nrow(tmp), as.vector(tmp$tf), function(pos, tmp) { :
arguments must have same length
In addition: Warning messages:
1: In data.frame(tf = factor(tmp[, 1]), target = factor(tmp[, 2]), :
NAs introduced by coercion
2: In data.frame(tf = factor(tmp[, 1]), target = factor(tmp[, 2]), :
NAs introduced by coercion

Steps Taken to Resolve the Issue:

I have checked the format of the TSV file and confirmed that all columns and data are correctly formatted.
I filtered out any potential NA values in the network file to ensure data consistency.
I verified that the gene names in both the expression matrix and the ARACNe network file match.

Relevant Code:

Load the expression matrix

exp.mat <- as.matrix(read.table("exp.cpm1.txt", sep = "\t", header = TRUE, row.names = 1))

Call the RegProcess function to process the ARACNe network file

RegProcess(a.file = "bootstrap.tsv",
exp.mat = exp.mat,
out.dir = "output/",
out.name = "regulon")

Details of the Troubleshooting Steps:

I ensured that the TSV file contains a header and that the data is formatted consistently.
I checked for duplicate row or column names and ensured that all input files use tab delimiters.
I confirmed that the expression matrix has no missing values and that all gene IDs are unique.

Help Requested:

I would like to know if this error could be related to the TSV file format or data consistency.
Are there any recommended ways to further debug this issue, or should I provide additional debugging information?
If there are similar issues or known solutions, I would appreciate some guidance.
Thank you very much for your help!