-
Notifications
You must be signed in to change notification settings - Fork 22
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
processBismark Error #84
Comments
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Hello,
I get an error message when I run the command line :
DMRichR::DM.R(genome = "dlabrax2021",testCovariate = "Condition", cores = 6)
Please note that I have modified the package to add my own genome.
I get the same message when I run this part of the script:
bs.filtered <- DMRichR::processBismark(files = list.files(path = getwd(), pattern = "*.CpG_report.txt.gz"), meta = openxlsx::read.xlsx("sample_info.xlsx", colNames = TRUE) %>% dplyr::mutate_if(is.character, as.factor), testCovariate = "Condition", adjustCovariate = NULL, matchCovariate = NULL, coverage = 1, cores = 6, perGroup = 0.75, sexCheck = FALSE)
Here's the message:
[DMRichR] Processing Bismark cytosine reports 25-04-2024 12:46:37
Selecting files...
Reading cytosine reports...
[read.bismark] Parsing files and constructing valid loci ...
Done in 42.8 secs
[read.bismark] Parsing files and constructing 'M' and 'Cov' matrices ...
Done in 45.4 secs
[read.bismark] Constructing BSseq object ...
Assigning sample metadata with Condition as factor of interest...
DataFrame with 10 rows and 1 column
Condition
FW-a1 FW-a
FW-a2 FW-a
FW-a3 FW-a
FW-a4 FW-a
FW-a5 FW-a
FW-i1 FW-i
FW-i2 FW-i
FW-i3 FW-i
FW-i4 FW-i
FW-i5 FW-i
Filtering CpGs for Condition...
Making coverage filter table...
Error in MatrixGenerics:::.load_next_suggested_package_to_search(x) :
Failed to find a rowSums2() method for list objects.
How can I solve this problem? I reinstalled the MatrixGenerics package but it didn't work.
Thank you for your help
The text was updated successfully, but these errors were encountered: