deconstructSigs错误

Question

I am using the deconstructSigs package and when I try to convert the mutation list to the correct input format I get this error:

Error in .local(x, ...) : 'start', 'end' and 'width' can only be specified when 'names' is either missing, a character vector/factor, a character-Rle, or a factor-Rle

This is my code:

library(deconstructSigs)
sigs.input <- mut.to.sigs.input(mut.ref = data, 
                                sample.id = "Gene_Symbol", 
                                chr = "Chromosome", 
                                pos = "Position", 
                                ref = "Reference_Base", 
                                alt = "Alternate_Base")

Does anyone know how to deal with it? Thanks in advance.

Answer 1

Not sure if this will match your issue, but I had the same problem when reading in a dataframe in "tibble" format. For me, the following solved the problem:

library(deconstructSigs)
sigs.input <- mut.to.sigs.input(mut.ref = data %>% as.data.frame(), 
                                sample.id = "Gene_Symbol", 
                                chr = "Chromosome", 
                                pos = "Position", 
                                ref = "Reference_Base", 
                                alt = "Alternate_Base")