absolute running error: Error in if (!is.na(res)) { : the condition has length > 1
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Entering edit mode
11 weeks ago
qiuting ▴ 20

The following are my R codes:

install.packages("numDeriv")
BiocManager::install("DNAcopy")
install.packages("ABSOLUTE_1.0.6.tar.gz",repos = NULL)
library(numDeriv)
library(ABSOLUTE)
RunAbsolute(
  seg.dat.fn = "P01_1_GISTIC_segment", 
  sigma.p = 0,
  max.sigma.h = 0.2,
  min.ploidy = 0.5, 
  max.ploidy = 8, 
  primary.disease = "NPC", 
  platform = "Illumina_WES", 
  results.dir = "P01_1", 
  sample.name = "P01_1", 
  max.as.seg.count = 1500, 
  max.neg.genome = 0.005,
  max.non.clonal = 1, 
  copy_num_type = "total",
  maf.fn = "P01_1_absolute.maf",
  min.mut.af = 0.05
)

I received an error:

Error in if (!is.na(res)) { : the condition has length > 1

I have no idea how to solve this error, can anyone suggest any solutions? I will appreciate it if someone can help me out

R ABSOLUTE • 252 views
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Entering edit mode

This is the error.log:

Detected error in sample P01_1 
Error message: the condition has length > 1 
Where:
if !is.na(res) {
    mode.tab[(i - 1) * n.d + j, ] <- c(res[[1]], res[[2]], res[[3]])
} 
Skipping this sample.
========
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