Correct file for sequenza.extract?

[bwubbe...@gmail.com]

I do not fully understand this methods pipeline but I was curios why in the example sequenza.extract is executed on the raw seqz data data.file, instead of the GC normalized data in the seqz.data variable (according to the usage example)

test <- sequenza.extract(data.file)

I had actually tried to run sequenza.extract on seqz.data but receive an error:

> test <- sequenza.extract(seqz.data) Error in pipe(paste("gzip -d -c", file, "| cut -f 1,6,10")) : invalid 'description' argument

Can anyone explain this to me in a bit further detail? Is there just something wrong with my data files or am I just making a poor assumption on what sequenza is actually doing? If sequenza.extract(data.file) is correct for real data then what purpose does the GC normalization steps serve? 

Thank you

[bwubbe...@gmail.com]

It turns out the sequenza.extract does the normalization and everything for you. This is why you can just run it on the input file.

[Matt Paul]

I am encountering the same error, when running it with my own file and with the example dataset. How did you overcome that error?

[Yihua Liu]

I am encountering an error, also came out from "sequenza.extract" function:

The error message it gave to me as : 

Processing chr1_GL456210_random: Error in data.frame(chrom, pos, wins.data, stringsAsFactors = FALSE) : 

  arguments imply differing number of rows: 27, 0

In addition: Warning message:

In numericChrom(chrom) : NAs introduced by coercion

Error in if (!is.null(breaks) & nrow(breaks) > 0) { : 

  argument is of length zero

Calls: sequenza.extract

Execution halted"

Actually, I have no idea what is that chromosome is. Is there a way we could choose chromosome 1-22 and X only and get rid of the rest of the chromosome?

Thanks~

Yihua