ABSOLUTE R package - CreateReviewObject Error, Error in seq_len(M) : argument must be coercible to non-negative integer

Question

[calvi.c]

Hi all,

I am using the R package ABSOLUTE and ran the function RunAbsolute .

My segment file (absolute.segment.numonly) looks like this:

Chromosome      Start   End     Num_Probes      Segment_Mean
chr1    13048   647355  77      0.0994
chr1    657939  909727  168     -0.921
chr1    909827  935126  15      -1.7359
chr1    943368  977419  32      -0.7704
chr1    978837  978887  3       -2.2057
chr1    978987  1019721 55      -0.8486
chr1    1019777 1248069 166     -1.273
chr1    1248169 1289627 105     -1.007
...

I replaced/deleted all chromosome names that are not in the format chr# or # as the GenePattern website (http://software.broadinstitute.org/cancer/software/genepattern/modules/docs/ABSOLUTE) says.

Now when I run RunAbsolute (works) and CreateReviewObject (apparently this throws the error) it creates the RData file, but not the plot (empty PDF file) and gives me the error "Error in seq_len(M) : argument must be coercible to non-negative integer"

I followed the answer of this (http://archive.broadinstitute.org/cancer/cga/node/668) topic of someone who set max.non.clonal to 0.1 but it did not work.

This is my code:

library(ABSOLUTE)
segfile="absolute.segment.numonly"
genome <- "hg19"
platform <- "Illumina_WES"
sigma.p <- 0.05
max.sigma.h <- 0.02
min.ploidy <- 0.95
max.ploidy <- 2
max.as.seg.count <- 1000000
max.non.clonal <- 0.1
max.neg.genome <- 0
copy_num_type <- "total"
sample.name="TGlioma"
primary.disease="Glioma"
results.dir ="results"

RunAbsolute(segfile, 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 = NULL, min.mut.af = NULL,
            output.fn.base = "absolute.output.malignant", verbose = TRUE)

Unfortunately, I get this error:

> source('~/ABSOLUTE.r')
[1] "Capping 0 segs at tCR = 5.0"
[1] "Expected copy-ratio = 0.95334"
[1] "MAF file:  not found."
.....................
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.....................
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-------
[1] "1d mode opt: "
     [,1]      [,2]      [,3]
[1,]    0 -2.287936 -5552.342
[2,]    0 -2.287936 -5552.342
[3,]    0 -2.287936 -5552.342
[4,]    0 -2.287936 -5552.342
[5,]    0 -2.287936 -5552.342
[6,]    0 -2.287936 -5552.342
[7,]    0 -2.287936 -5552.342
[1] "4 unique modes found"
[1] "1 modes in b / delta range."
     alpha      tau AT b     delta       LL mode_curv
[1,]     1 9.874938 NA 0 0.1012665 5552.445 -8.166027
[1] "removing 1 / 1 modes outside of alpha/tau range."
[1] "Evaluating subclonal SCNAs in  purity/ploidy modes: "

Error in seq_len(M) : argument must be coercible to non-negative integer
In addition: There were 50 or more warnings (use warnings() to see the first 50)

How can this problem be solved?

Thanks!

[calvi.c]

What I also don t understand is - when I use a different value for max.non.clonal (like 0 or 1) then I get a different error message...

source('~/ABSOLUTE.r')
[1] "Capping 0 segs at tCR = 5.0"
[1] "Expected copy-ratio = 0.95334"
[1] "MAF file:  not found."
.....................
.....................
.....................
.....................
.....................
.....................
.....................
.....................
.....................
-------
[1] "1d mode opt: "
     [,1]       [,2]      [,3]
[1,]    0 -2.4401744 -12959.73
[2,]    0 -0.6523878 -35730.61
[3,]    0 -2.4401759 -12959.73
[4,]    0 -0.3623117 -36638.76
[5,]    0 -2.4401744 -12959.73
[6,]    0 -2.4401744 -12959.73
[7,]    0 -2.4401759 -12959.73
[1] "11 unique modes found"
[1] "3 modes in b / delta range."
[1] "WARNING: NON-FINITE log_evidence"
     alpha       tau AT b      delta       LL mode_curv
[1,]     1 11.473041 NA 0 0.08716085 12959.76       NaN
[2,]     1  1.915541 NA 0 0.52204578 35732.87 -11.19443
[3,]     1  1.433329 NA 0 0.69767633 36642.09 -12.11249
[1] "removing 1 / 3 modes outside of alpha/tau range."
[1] "Optimizing LL(data, theta.qz, sigma.h | comb) for 2 modes: "
SSSSSSSSS[1] "Warning: NaN loglik in opt_theta_Z_sigma_H"
    sigma.h.hat=0.01964
SSSSSSSSS[1] "Warning: NaN loglik in opt_theta_Z_sigma_H"
    sigma.h.hat=0.01964
[1] "Evaluating subclonal SCNAs in 2 purity/ploidy modes: "
[1] "Switching to total copy Karyotype model..."
[1] "Switching to total copy Karyotype model..."
[1] "Switching to total copy Karyotype model..."
[1] "Switching to total copy Karyotype model..."
Error in 1:n.print[!ix] : argument of length 0
In addition: There were 50 or more warnings (use warnings() to see the first 50)

Answer 1

[markus.riester]

I cannot comment on the crash, but I recommend reading the ABSOLUTE, ASCAT and more recent papers like Sequenza. Running ABSOLUTE with only segmented data is pretty much futile. You need germline allelic fractions to determine the number of maternal and paternal copy numbers, which are also necessary to identify the sample ploidy. There are recent papers for which they used ABSOLUTE on sequencing data, maybe checking the corresponding method sections will help. There are also plenty of alternatives like Sequenza.