ABSOLUTE error, calulate tumor purity Error in GetLambda
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5.9 years ago

I'm using the ABSOLUTE to run tumor purity, and set the parameters to this:

args <- commandArgs()
library(ABSOLUTE)
sigma.p <- 0
max.sigma.h <- 0.02
min.ploidy <- 0.95
max.ploidy <- 10
max.as.seg.count <- 450000
max.non.clonal <- 0
max.neg.genome <- 0
platform <- 'Illumina_WES'
results.dir <- args[5]
copy_num_type <- "total"
primary.disease <- "Lung"
sample.name <- args[4]
cnv <- args[6]
snv <- args[7]

RunAbsolute(cnv, sigma.p, max.sigma.h, min.ploidy, max.ploidy, primary.disease, platform, sample.name, results.dir, max.as.seg.count, max.non.clonal, max.neg.genome, copy_num_type, maf.fn=snv, min.mut.af=0.01, verbose=TRUE)

But there are 3 samples got the following errore:

Error in GetLambda(theta.qz.hat, obs[["W"]], max.q + 1, verbose = verbose) :

Calls: RunAbsolute -> FitSample -> OptThetaQzSigmaH -> GetLambda

Execution halted

Would someone help me with this?

myposts R Tumor Purity • 1.7k views
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