Ploidy with max SLPP is not choosed by Sequenza automatically

[11033...@qq.com]

Hi,

I am using Sequenza on WES data.I remember that Sequenza will choose the solution with max SLPP value automatically, and use that ploidy to plot genome_view.pdf and generate segments.txt. But this time I find the solution choosed by Sequenza is not the one with max SLPP. I wonder if there is any change in v3.0.0.

Below is my code:

library(sequenza)
library(copynumber)
input_dir <- 'F:\\xiehe_ecc\\seqz_result\\'
output_dir <- 'F:\\xiehe_ecc\\seqz_cnv\\'
files <- dir(input_dir)
chromosome_list <- paste('chr', as.character(1:22), sep = '')
for(file in files){
  sample <- strsplit(file, '\\.')[[1]][1]
  dir.create(paste(output_dir, sample, sep = ''))
  data <- sequenza.extract(paste(input_dir, file, sep = ''), chromosome.list = chromosome_list)
  data.cp <- sequenza.fit(data)
  sequenza.results(sequenza.extract = data, cp.table = data.cp, sample.id = sample, chromosome.list = chromosome_list, out.dir = paste(output_dir, sample, sep = ''))
}

Attached is the alternative solutions for one sample, as you can see, the ploidy with max SLPP is around 2, but the genome_view and CN_bars seems like 3-4 (ploidy).

By the way, I want to know how is ploidy calculated in Sequenza. I tried to calculate ploidy myselt using the segment file:

ploidy = sum(CNt * (end.pos - start.pos)) / sum(end.pos - start.pos)

but the ploidy I get is 3.146, not 2.2 or 3.4 in alternative solutions.

I would appreciate if you could give me some advice. Thank you!

Yang

[pin wu]

Hi Yang,

Has this problem been resolved? I also encountered the same problem with sequenza v 2.0.

Best,

Pin

在 2019年7月3日星期三 UTC+8下午4:32:26，11033...@qq.com写道：

[pin wu]

Hi Yang,

I'm sorry to reply to you so late. Sequenza uses the BAF model to calculate ploidy and purity with max SLPP, which takes into account many factors instead of just using the formula you provided. If you want to simply calculate the ploidy of the sample based on the results of sequenza, I think the more common method is to set the copy number value (the largest proportion of the genomic region with this copy number value) as the ploidy of the sample. Then the sample's ploidy is an integer.

Best,

Pin

pin wu <biow...@gmail.com> 于2020年3月8日周日 下午5:01写道：

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