【无标题】Error: The input GRanges (your vcf data) and the ref_genome do not have the same genome

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于 2023-05-17 22:25:08 发布

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在R中处理基因组数据时，遇到一个错误，由于输入的GRanges对象genomename为NA，与ref_genome的hg38不匹配。通过使用GenomeInfoDb包设置GRanges的genomename为hg38，解决了这个问题，使得mut_context函数能够正常运行。

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报错

>ref_genome <- "BSgenome.Hsapiens.UCSC.hg38.masked"
>  library(ref_genome, character.only = T)

>  curr.granges <- makeGRangesFromDataFrame(curr,
                                           seqnames.field = "Chr",
                                           start.field= "Start",
                                           end.field = "End",
                                           keep.extra.columns = T)
>curr.granges$trinucleotide <- mut_context(curr.granges, ref_genome)
Error: The input GRanges (your vcf data) and the ref_genome do not have the same genome name.
This problem is known to occur when you use an outside function to read in vcfs.
The input GRanges has the genome name: 'NA'
The ref_genome has the genome name: 'hg38'
With `GenomeInfoDb::genome(your input GRanges) = 'hg38'`
you can view and change the genome name of your data to that of the ref_genome.

解决方案：

>GenomeInfoDb::genome(curr.granges)='hg38'

>curr.granges$trinucleotide <- mut_context(curr.granges, ref_genome)

ok，可以正常运行