Closed laurasteinmann closed 4 years ago
Hi, Thank you for using the Pipeline. This error is because of converting data types. Please modify these lines of code in "src/bash/methimpute.R" file, should be solve the problem. (~ lines 34-40) (Please add Bold lines) Change into: ` ........ df <- df %>% mutate_if(is.factor, as.character)
df$seqnames <-as.character(df$seqnames)
col.names <- c("seqnames","start","context.trinucleotide") Cx <- fread(original_file, skip=0, sep='\t', col.names =col.names, select=c(1,2,7), stringsAsFactors = FALSE )
Cx$seqnames <-as.character(Cx$seqnames)
final_dataset <- df %>% left_join(Cx, by = c("seqnames", "start")) ` Please let me know if you solved this problem then I can fix the bug and will update the package.
Thank you very much for your help. With the two extra lines of code it works now.
Hi, thank your for your really helpful Pipeline. I try to use the Pipeline in your prepared Docker but I just get stuck with a Error Message in the Methimpute-Part:
I use a customized Arabidopsis reference genome without mitochondrial and chloroplast sequences. Can you tell me which files causes the Error so I can look at them more closely? I just can't find this in your code. Or do you even had the same problem once? Thank you very much Laura