![]() However, I expected the new variants to be added to the MAF object. The issue I'm encountering is that after running this code, the total variants I find in and are exactly the same. Oncoplot(maf= Z, top = 200, fontSize = 0.3) Save(merged_MAF, file = "FGFR3_Rick.rda")įILE <- list.files(pattern = "FGFR3_RICK.maf") Merged_MAF <- new_variants_df, fill=TRUE) Protein_position=fgfr3_status$`protein pos`,Įxisting_variation= fgfr3_status$`Known var`, ![]() ![]() Sequence_Source = fgfr3_status$`Seq type`, Match_Norm_Seq_Allele1 = fgfr3_status$Alt, Tumor_Sample_Barcode = fgfr3_status$Sample, Tumor_Seq_Allele2 = fgfr3_status$Tum_Alt, Tumor_Seq_Allele1 = fgfr3_status$Tum_Ref, Variant_Classification = fgfr3_status$consequence, Here's the code I have tried so far: setwd("path/to/folder/")Īdd_count(Hugo_Symbol, Transcript_ID, Tumor_Sample_Barcode, Chromosome, Start_Position, Variant_Classification)Įntrez_Gene_Id = NA, # You might need to add NA values for columns not present in the metadataĮnd_Position = NA, # You might need to add NA values for columns not present in the metadata However, I am unsure if the data in this table contains all the necessary information to meet the requirements for filling the MAF file. Sample chrom Pos Ref Alt var_type consequence Impact `cDNA pos` `CDS pos` `protein pos` `AA pos` `codon change` SIFT `Known var` Tum_Ref Tum_Alt Tum_VAF `Seq type` These are my table columns, I'd like to add to my MAF: > head(fgfr3_status) The MAF file I have is entirely generated from WES (Whole Exome Sequencing) data. The aim is to oncoplot properly this gen. I am relatively new to bioinformatics, and I need some help with adding variants from a specific gene that were sequenced using amplicon data (due to bad sequencing in a hot spot) to a MAF (Mutation Annotation Format) file.
0 Comments
Leave a Reply. |
AuthorWrite something about yourself. No need to be fancy, just an overview. ArchivesCategories |