Hi Diffbind community!
I have been encountering some errors creating dba object because the Diffbind package can not load the files. I tried using the aligned bam files after creating sample sheet but have been getting following error:
"Error in if ((length(callers) == 1) & (callers[1] == "counts")) { : argument is of length zero"
This was my sample sheet creation: Sampleinfo <- data.frame( SampleID = c("CR-clear2_CRR711256", "AL-clear2_CRR711253", "AL-clear2_CRR711254", "CR-clear2_CRR711255"), condition = c("CR", "AL", "CR", "AL"), Treatment = c("Treated", "Unreated"), Filename = c( "/Users/kuldeepmakwana/Documents/ATAC-seq-CRA010174/CR/Clear_files/CR-clear2_CRR711256.bam", "/Users/kuldeepmakwana/Documents/ATAC-seq-CRA010174/AL/clean/AL-clear2_CRR711253.bam", "/Users/kuldeepmakwana/Documents/ATAC-seq-CRA010174/CR/Clear_files/CR-clear2_CRR711255.bam", "/Users/kuldeepmakwana/Documents/ATAC-seq-CRA010174/AL/clean/AL-clear2_CRR711254.bam" ) )
I checked for file existence, file path error but everything seems to be working fine. Tried uninstalling and reinstalling the package but all in vain.
I then tried to load the narrow peak out put from the macs2 but diffbind is not loading the files
setwd("/Users/kuldeepmakwana/Documents/ATAC_seq_CRA010174/CR/Clear_files") sample = read.csv("Book1.csv") dba <- dba.load(sample)
Error in gzfile(file) : invalid 'description' argument
Please if someone can help me figure this out. Your help is much appreciated
