Question: ABSOLUTE MAF error
0
gravatar for Alejandro Jimenez Sanchez
3.0 years ago by
Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK

I am running ABSOLUTE 1.0.6 in R 3.4.0

When I do:

RunAbsolute(seg.dat.fn, 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, min.mut.af, output.fn.base=NULL, verbose=TRUE)

I get:

[1] "Capping 1 segs at tCR = 5.0"
[1] "Expected copy-ratio = 0.89228"
[1] "Removing 0 of 42303 mutations with NA coverage"
[1] "Removing NA of 42303 mutations due to allelic fraction < 0"
[1] "Removing 0 mutations in IG regions" 
Error in if (sum(seg.ix) != 1) { : missing value where TRUE/FALSE needed

If I do:

maf.fn <- NULL

Everything runs smoothly, so the error should be in the MAF file.

The headers of the MAF are:

   'Hugo_Symbol', 'Entrez_Gene_Id', 'Center', 'NCBI_Build',
   'Chromosome', 'Start_position', 'End_position', 'Strand',
   'Variant_Classification', 'Variant_Type', 'Reference_Allele',
   'Tumor_Seq_Allele1', 'Tumor_Seq_Allele2', 'dbSNP_RS',
   'dbSNP_Val_Status', 'Tumor_Sample_Barcode',
   'Matched_Norm_Sample_Barcode', 'Match_Norm_Seq_Allele1',
   'Match_Norm_Seq_Allele2', 'Tumor_Validation_Allele1',
   'Tumor_Validation_Allele2', 'Match_Norm_Validation_Allele1',
   'Match_Norm_Validation_Allele2', 'Verification_Status',
   'Validation_Status', 'Mutation_Status', 'Sequencing_Phase',
   'Sequence_Source', 'Validation_Method', 'Score', 'BAM_File',
   'Sequencer', 'Tumor_Sample_UUID', 'Matched_Norm_Sample_UUID',
   'HGVSc', 'HGVSp', 'HGVSp_Short', 'Transcript_ID', 'Exon_Number',
   't_depth', 't_ref_count', 't_alt_count', 'n_depth', 'n_ref_count',
   'n_alt_count', 'all_effects', 'Allele', 'Gene', 'Feature',
   'Feature_type', 'Consequence', 'cDNA_position', 'CDS_position',
   'Protein_position', 'Amino_acids', 'Codons', 'Existing_variation',
   'ALLELE_NUM', 'DISTANCE', 'STRAND_VEP', 'SYMBOL', 'SYMBOL_SOURCE',
   'HGNC_ID', 'BIOTYPE', 'CANONICAL', 'CCDS', 'ENSP', 'SWISSPROT',
   'TREMBL', 'UNIPARC', 'RefSeq', 'SIFT', 'PolyPhen', 'EXON', 'INTRON',
   'DOMAINS', 'GMAF', 'AFR_MAF', 'AMR_MAF', 'ASN_MAF', 'EAS_MAF',
   'EUR_MAF', 'SAS_MAF', 'AA_MAF', 'EA_MAF', 'CLIN_SIG', 'SOMATIC',
   'PUBMED', 'MOTIF_NAME', 'MOTIF_POS', 'HIGH_INF_POS',
   'MOTIF_SCORE_CHANGE', 'IMPACT', 'PICK', 'VARIANT_CLASS', 'TSL',
   'HGVS_OFFSET', 'PHENO', 'MINIMISED', 'ExAC_AF', 'ExAC_AF_AFR',
   'ExAC_AF_AMR', 'ExAC_AF_EAS', 'ExAC_AF_FIN', 'ExAC_AF_NFE',
   'ExAC_AF_OTH', 'ExAC_AF_SAS', 'GENE_PHENO', 'FILTER',
   'flanking_bps', 'variant_id', 'variant_qual', 'ExAC_AF_Adj',
   'ExAC_AC_AN_Adj', 'ExAC_AC_AN', 'ExAC_AC_AN_AFR', 'ExAC_AC_AN_AMR',
   'ExAC_AC_AN_EAS', 'ExAC_AC_AN_FIN', 'ExAC_AC_AN_NFE',
   'ExAC_AC_AN_OTH', 'ExAC_AC_AN_SAS', 'ExAC_FILTER'

I want to run ABSOLUTE with the MAF to include the SNV information. Does anyone know how to solve the error generated when the MAF file is included?

Thanks, Alejandro

absolute maf • 1.8k views
ADD COMMENTlink modified 23 months ago by kmvaldez210 • written 3.0 years ago by Alejandro Jimenez Sanchez120

Could be wrong, but I think p in Start_position and End_position should start with uppercase. Start_Position End_Position

ADD REPLYlink written 3.0 years ago by poisonAlien2.8k

Thanks for your comment. Indeed the original MAF file had it with uppercase, but when I run it I get the following error:

Error in `[.data.frame`(maf, , "Start_position") : 
undefined columns selected

Thus, I changed Start_Position to Start_position, the same for End_position. Then I get the error:

Error in if (sum(seg.ix) != 1) { : missing value where TRUE/FALSE needed

Which is the question posted. If you have any other idea why this error may be, please let me know. :)

ADD REPLYlink written 3.0 years ago by Alejandro Jimenez Sanchez120

Absolute requires column containing vaf, t_vaf. Maybe try adding it ?

maf$t_vaf = as.numeric(as.character(maf$t_alt_count)) / as.numeric(as.character(maf$t_depth))

edit: also make sure chromosome names in MAF matches to that in segmentatioin file. Better remove chr prefix from both files.

ADD REPLYlink modified 3.0 years ago • written 3.0 years ago by poisonAlien2.8k

I added t_vaf and make sure that the chromosome names were the same between the MAF and the seg file. I should say that the data I am trying to analyse is mouse data, and when I run human data I don't have the problem. I know Absolute was developed for human data, but I was giving it a try. I want to get absolute copy numbers, purity, and clonality of this mouse data, so I was thinking in another tool such as FACETS, which can use mouse data.

Best, Alejandro

ADD REPLYlink modified 3.0 years ago • written 3.0 years ago by Alejandro Jimenez Sanchez120

oh ! Okay, I think Absolute uses pre-computed purity and ploidy models from known cancer cohorts. I guess this is an issue if you're using non-human genome.

ADD REPLYlink written 3.0 years ago by poisonAlien2.8k

Hello,

Were you able to resolve this issue?

I am having the same error using human cancer samples on Absolute v1.0.6. I also adjusted my MAF column headers, added the t_vaf column, and removed the 'chr' prefix for the Chromosome column.

Thanks!

ADD REPLYlink written 2.9 years ago by emilie.lalonde0

Hi,

With human samples everything ran smoothly. Maybe if you want, send me the first ~ 50 rows of your MAF and I can try to run it with my script...

ADD REPLYlink modified 2.9 years ago • written 2.9 years ago by Alejandro Jimenez Sanchez120

Hi . I also encounter this issue. RunAbsolute works well locally,but when qsub to cluster,it returned the same error. Do you have any idea? thx.

ADD REPLYlink written 2.9 years ago by reany0
0
gravatar for kmvaldez2
2.0 years ago by
kmvaldez210
kmvaldez210 wrote:

I had a similar error in my run, it was caused by the mitochondrial 'chromosome' MT in my segmented_copy_ratios file not being an integer.

I understand that the original post was referring to the MAF, but check for this if you run into an issue with the seg file. I was going crazy trying to figure out what my error meant!

ADD COMMENTlink written 2.0 years ago by kmvaldez210
0
gravatar for kmvaldez2
23 months ago by
kmvaldez210
kmvaldez210 wrote:

Also, none of the rows in the maf file can have a value of zero in BOTH t_alt_count AND t_ref_count.

Try something like the following to exclude them:

maf = maf[!(maf$t_alt_count==0 & maf$t_ref_count==0),]
ADD COMMENTlink modified 23 months ago • written 23 months ago by kmvaldez210
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