Create mutation catalogue function giving GRange object errors
Entering edit mode
22 months ago
kittys • 0

Hi, I am trying to analyse indel mutations using the R package YAPSA. My data is in the input format required, with columns chrom, pos, ref, alt and patient ID. I am trying to use the function create_mutation_catalogue_from_df with this data using the GRCh38 of the genome. My command is:

indel_catalogue <- create_mutation_from_df(indels_df, this_seqnames.field = "chrom", this_start.field = "pos", this_end.field = "pos", this_PID.field = "patient_ID", this_refGenome = BSgenome.Hsapiens.NCBI.GRCh38, this_verbose = 1)

The error I get is: Error in validObject(.Object) : invalid class "GRanges" object : 'seqnames(x)' contains missing values

I also tried adding: this_refGenome_Seqinfo = seq_info_GRCh38 where seq_info_GRCh38 <- SeqinfoForBSGenome(BSgenome.Hapsiens.NCBI.GRCh38)

I tried the translate_to_hg19 function before running the command with no success either.

I also tried this with the BSgenome.Hsapiens.UCSC.hg38 genome which returns the error error in ans[] <- x : replacement has length zero

Any ideas on how to fix this? Any suggestions would be hugely appreciated!! Thank you :)

YAPSA GenomicRanges R indels • 454 views

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