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PoisonAlien / maftools

Summarize, Analyze and Visualize MAF files from TCGA or in-house studies.
http://bioconductor.org/packages/release/bioc/html/maftools.html
MIT License
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problem on TITV plot #385

Closed a00101 closed 5 years ago

a00101 commented 5 years ago

I manually maf file from raw VCF, vep annotated VCF and annovar results.


Tumor_Sample_Barcode | Chromosome | Start_Position | End_Position | Reference_Allele | Tumor_Seq_Allele2 | Hugo_Symbol | Variant_Classification | tx | exon | txChange | aaChange | Variant_Type | Func.ensGene | Gene.ensGene | GeneDetail.ensGene | ExonicFunc.ensGene | AAChange.ensGene | ENSGID | SIFT_PRED | SIFT_SCORE | POLYPHEN_PRED | POLYPHEN_SCORE | MA_PRED | MA_SCORE | rsID | NORMAL_AF | TUMOR_AF
-- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | --
test1 | chr1 | 125861 | 125861 | AAC | AAC | RP11-34P13.7 | unknown | ENST00000466430.5 |   |   | DEL | ncRNA_intronic | RP11-34P13.7 | . | . | . | ENSG00000238009 |   |   |   |   |   | rs756031404 | 0 | 0.063
test1 | chr1 | 950141 | 950141 | G | G | NOC2L | unknown | ENST00000327044.7 |   |   | SNP | intronic | NOC2L | . | . | . | ENSG00000188976 |   |   |   |   |   |   | 0 | 0.184
test1 | chr1 | 1285177 | 1285177 | C | C | SCNN1D | unknown | ENST00000379116.9 |   |   | SNP | intronic | SCNN1D | . | . | . | ENSG00000162572 |   |   |   |   |   |   | 0 | 0.152
test1 | chr1 | 1963311 | 1963311 | C | C | CFAP74 | unknown | ENST00000493964.5 |   |   | SNP | intronic | CFAP74 | . | . | . | ENSG00000142609 |   |   |   |   |   | rs914658862 | 0 | 0.22


> manual_maf = "test.maf"
> maffile = read.maf(maf=manual_maf)
-Reading
-Validating
--Non MAF specific values in Variant_Classification column:
  unknown
-Silent variants: 8974 
-Summarizing
-Processing clinical data
--Missing clinical data
-Finished in 0.160s elapsed (0.110s cpu) 
> plotmafSummary(maf=maffile)
Error in dcast.data.table(data = maf.con.class.summary, formula = Tumor_Sample_Barcode ~  : 
  Can not cast an empty data.table
In addition: Warning message:
In titv(maf = maf, useSyn = TRUE, plot = FALSE) :
  Non standard Ti/Tv class: 7975TRUE

Help me to run successfully.

Thank you for your generousness.

a00101 commented 5 years ago

I mistake the process of maffile. Ref is the same with Alt.

Thanks me.