Closed bioinfo-dirty-jobs closed 6 years ago
PoisonAlien
commented
6 years ago You should provide column name containing vaf values as an argument to vafCol.
I think there is no column by name i_TumorVAF_WU in your merged maf file? Use getFields to see available column names in maf object.
bioinfo-dirty-jobs
commented
6 years ago @PoisonAlien thanks so mcuh for the hel Here you have the columns:
getFields(sar2)
[1] "Hugo_Symbol" "Entrez_Gene_Id"
[3] "Center" "NCBI_Build"
[5] "Chromosome" "Start_Position"
[7] "End_Position" "Strand"
[9] "Variant_Classification" "Variant_Type"
[11] "Reference_Allele" "Tumor_Seq_Allele1"
[13] "Tumor_Seq_Allele2" "dbSNP_RS"
[15] "dbSNP_Val_Status" "Tumor_Sample_Barcode"
[17] "Matched_Norm_Sample_Barcode" "Match_Norm_Seq_Allele1"
[19] "Match_Norm_Seq_Allele2" "Tumor_Validation_Allele1"
[21] "Tumor_Validation_Allele2" "Match_Norm_Validation_Allele1"
[23] "Match_Norm_Validation_Allele2" "Verification_Status"
[25] "Validation_Status" "Mutation_Status"
[27] "Sequencing_Phase" "Sequence_Source"
[29] "Validation_Method" "Score"
[31] "BAM_File" "Sequencer"
[33] "Tumor_Sample_UUID" "Matched_Norm_Sample_UUID"
[35] "HGVSc" "HGVSp"
[37] "HGVSp_Short" "Transcript_ID"
[39] "Exon_Number" "t_depth"
[41] "t_ref_count" "t_alt_count"
[43] "n_depth" "n_ref_count"
[45] "n_alt_count" "all_effects"
[47] "Allele" "Gene"
[49] "Feature" "Feature_type"
[51] "Consequence" "cDNA_position"
[53] "CDS_position" "Protein_position"
[55] "Amino_acids" "Codons"
[57] "Existing_variation" "ALLELE_NUM"
[59] "DISTANCE" "STRAND_VEP"
[61] "SYMBOL" "SYMBOL_SOURCE"
[63] "HGNC_ID" "BIOTYPE"
[65] "CANONICAL" "CCDS"
[67] "ENSP" "SWISSPROT"
[69] "TREMBL" "UNIPARC"
[71] "RefSeq" "SIFT"
[73] "PolyPhen" "EXON"
[75] "INTRON" "DOMAINS"
[77] "GMAF" "AFR_MAF"
[79] "AMR_MAF" "ASN_MAF"
[81] "EAS_MAF" "EUR_MAF"
[83] "SAS_MAF" "AA_MAF"
[85] "EA_MAF" "CLIN_SIG"
[87] "SOMATIC" "PUBMED"
[89] "MOTIF_NAME" "MOTIF_POS"
[91] "HIGH_INF_POS" "MOTIF_SCORE_CHANGE"
[93] "IMPACT" "PICK"
[95] "VARIANT_CLASS" "TSL"
[97] "HGVS_OFFSET" "PHENO"
[99] "MINIMISED" "ExAC_AF"
[101] "ExAC_AF_AFR" "ExAC_AF_AMR"
[103] "ExAC_AF_EAS" "ExAC_AF_FIN"
[105] "ExAC_AF_NFE" "ExAC_AF_OTH"
[107] "ExAC_AF_SAS" "GENE_PHENO"
[109] "FILTER" "flanking_bps"
[111] "variant_id" "variant_qual"
[113] "ExAC_AF_Adj" "ExAC_AC_AN_Adj"
[115] "ExAC_AC_AN" "ExAC_AC_AN_AFR"
[117] "ExAC_AC_AN_AMR" "ExAC_AC_AN_EAS"
[119] "ExAC_AC_AN_FIN" "ExAC_AC_AN_NFE"
[121] "ExAC_AC_AN_OTH" "ExAC_AC_AN_SAS"
[123] "ExAC_FILTER" "MUTECT2"
```I try also to create t_vaf column t_alt_count'/t_ref_count' but however not workI see that you dont have a t_vaf column, but plotVaf will crate one for you since you already have t_ref_count and t_alt_count.
Run your command again without vafCol
plotVaf(maf = laml, vafCol = NULL)@PoisonAlien I have this error
Error in eval(.massagei(isub), x, parent.frame()) :
object 'value' not found
> sessionInfo()
R version 3.5.0 (2018-04-23)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1
locale:
[1] C
attached base packages:
[1] parallel stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] maftools_1.7.05 Biobase_2.40.0 BiocGenerics_0.26.0
loaded via a namespace (and not attached):
[1] httr_1.3.1 bit64_0.9-7
[3] splines_3.5.0 foreach_1.4.4
[5] assertthat_0.2.0 stats4_3.5.0
[7] blob_1.1.1 BSgenome_1.48.0
[9] GenomeInfoDbData_1.1.0 Rsamtools_1.32.0
[11] slam_0.1-43 progress_1.2.0
[13] ggrepel_0.8.0 pillar_1.2.3
[15] RSQLite_2.1.1 lattice_0.20-35
[17] digest_0.6.15 GenomicRanges_1.32.3
[19] RColorBrewer_1.1-2 XVector_0.20.0
[21] colorspace_1.3-2 cowplot_0.9.2
[23] Matrix_1.2-14 plyr_1.8.4
[25] pkgconfig_2.0.1 XML_3.98-1.11
[27] bibtex_0.4.2 GetoptLong_0.1.7
[29] biomaRt_2.36.1 zlibbioc_1.26.0
[31] xtable_1.8-2 scales_0.5.0
[33] BiocParallel_1.14.1 tibble_1.4.2
[35] pkgmaker_0.27 IRanges_2.14.10
[37] ggplot2_2.2.1 withr_2.1.2
[39] SummarizedExperiment_1.10.1 GenomicFeatures_1.32.0
[41] lazyeval_0.2.1 mclust_5.4
[43] crayon_1.3.4 survival_2.42-3
[45] magrittr_1.5 memoise_1.1.0
[47] doParallel_1.0.11 changepoint_2.2.2
[49] NMF_0.21.0 prettyunits_1.0.2
[51] tools_3.5.0 registry_0.5
[53] data.table_1.11.4 hms_0.4.2
[55] GlobalOptions_0.1.0 matrixStats_0.53.1
[57] gridBase_0.4-7 ComplexHeatmap_1.18.1
[59] stringr_1.3.1 S4Vectors_0.18.3
[61] munsell_0.5.0 cluster_2.0.7-1
[63] rngtools_1.3.1 DelayedArray_0.6.0
[65] AnnotationDbi_1.42.1 Biostrings_2.48.0
[67] compiler_3.5.0 GenomeInfoDb_1.16.0
[69] rlang_0.2.1 grid_3.5.0
[71] RCurl_1.95-4.10 iterators_1.0.9
[73] VariantAnnotation_1.26.0 rjson_0.2.20
[75] circlize_0.4.4 bitops_1.0-6
[77] gtable_0.2.0 codetools_0.2-15
[79] DBI_1.0.0 R6_2.2.2
[81] reshape2_1.4.3 gridExtra_2.3
[83] zoo_1.8-2 GenomicAlignments_1.16.0
[85] rtracklayer_1.40.3 bit_1.1-14
[87] shape_1.4.4 stringi_1.2.3
[89] Rcpp_0.12.17 wordcloud_2.5 Okay, as a last try - can you read your maf file freshly again and run the above command. If you still get the error then do the following to manually add vaf column,
sar2 = data.table::fread("path/to/merged.maf")
sar2[,t_vaf := as.numeric(t_alt_count)/(sum(as.numeric(t_alt_count) + as.numeric(t_alt_count))]
sar2 = maftools::read.maf(sar2)
plotVaf(maf = sar2)data.table is the package used by maftools for data processing. Sorry I just noticed I had made a typo in above command. I have corrected it. You can try and let me know.
bioinfo-dirty-jobs
commented
6 years ago @PoisonAlien Thanks so much!!!
sar2<-data.table::read("IMAGE/MUTECT2.vaf.maf.tsv")
Error: 'read' is not an exported object from 'namespace:data.table'
check my comment again, I have made corrections to it. It should be fread not read
bioinfo-dirty-jobs
commented
6 years ago @PoisonAlien
> sar2<-data.table::fread("IMAGE/MUTECT2.vaf.maf.tsv")
> sar2[,t_vaf:=as.numeric(t_alt_count)/(sum(as.numeric(t_alt_count) + as.numeric(t_alt_count))]
Error: unexpected ']' in "sar2[,t_vaf:=as.numeric(t_alt_count)/(sum(as.numeric(t_alt_count) + as.numeric(t_alt_count))]"
> Hi Sorry for the delay. Were you able to fix it ? You can attach your maf file here - maybe top 100 lines or so, I might be able to help you.
bioinfo-dirty-jobs
commented
6 years ago @PoisonAlien Thanks s match for the help! https://www.dropbox.com/s/axd25paqejmhs7z/mitico.maf.tsv?dl=0
PoisonAlien
commented
6 years ago Hi, Please attach it as a text file. Its not possible for me to parse your text.
bioinfo-dirty-jobs
commented
6 years ago @PoisonAlien Sorry I inser a link (https://www.dropbox.com/s/axd25paqejmhs7z/mitico.maf.tsv?dl=0)
PoisonAlien
commented
6 years ago Hi,
plotVaf wofks fine with you toy data.
> m = read.maf(maf = "~/Downloads/mitico.maf.tsv")
> plotVaf(maf = m)
t_vaf field is missing, but found t_ref_count & t_alt_count columns. Estimating vaf..
Could you try again ? Just read your maf and plot it, it should work.
bioinfo-dirty-jobs
commented
6 years ago @PoisonAlien I maybe found the problem.. What I send you it is only one art of the files. The problem are related on the varscan maf file. Inside the vaue onf t_alt_count are present % simbol. That is the problem
t_depth | t_ref_count | t_alt_count | n_depth | n_ref_count | n_alt_count
-- | -- | -- | -- | -- | --
22 | 2 | 20% | 15 | 0 | 0%I see. Sorry, you will have to manually correct them as there is no way of guessing type of values in vaf_col :|
I have created ma file starting from mutect2 smatic vcf using vcf2maf. Seem works. I concatenate 6 maf on a single file and I import on maftools. When I try to do this plot
I realize there is not VAF value. Is it normal? How to resolve?