I am doing research using sequenza. It is very useful and powerful tools.
But, I have some questions of sequenza using WGS. Using sequenza.extract, it has some error in R.
I used this code:
library(sequenza) library(copy number) data.file=paste0("12TB.seqz.edit.gz") test = sequenza.extract(data.file, verbose=FALSE, assembly="hg19")
Error message is:
Warning: 8 parsing failures. row col expected actual file 1 position an integer position '12TB.seqz.edit.gz' 1 depth.normal an integer depth.normal '12TB.seqz.edit.gz' 1 depth.tumor an integer depth.tumor '12TB.seqz.edit.gz' 1 depth.ratio a double depth.ratio '12TB.seqz.edit.gz' 1 Af a double Af '12TB.seqz.edit.gz' ... ............ .......... ............ ................... See problems(...) for more details.
Error in seq.int(range.pos[1], range.pos[2], by = window.offset) : 'to' must be a finite number In addition: Warning messages: 1: In read_tokens_(data, tokenizer, col_specs, col_names, locale_, : NAs introduced by coercion to integer range 2: In min(x) : no non-missing arguments to min; returning Inf
It doesn’t have error using Whole exome sequencing data.
I have no idea what kind of part is wrong.
Please let me know how to fix this error.
Thank you.
