ABSOLUTE R package - CreateReviewObject Error

[Calvi C.]

Hi all,

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

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)

output_path="results/absolute.output.malignant.ABSOLUTE.RData"

CreateReviewObject("Review_malignant", output_path,
                   paste(results.dir,"/run1",sep=""), "total", plot.modes = TRUE, 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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-------
[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!

[Barbara Hill]

Hello, 

Are you running this from the command line?

I would suggest the following contacts for help with this:

• For ABSOLUTE questions:
  • Use the Biostars forum <https://www.biostars.org/t/absolute/>
  • Use the CGA discussion and help forum, especially for help with data interpretation 
• The module is provided for academic non-commercial research purposes only. Other parties interested in using ABSOLUTE should contact the authors at <absolu...@broadinstitute.org>.

Best
Barbara