Question: Error running Genomic Vis vcf.venn(vcf.files, 'GRCh38', sample.names)
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3 months ago by
esimonova.me0 wrote:

I am trying to draw venn diagrams with a package GenomicVis package.

library(GenomicVis)

It is loaded with a warining:

Warning messages:
1: replacing previous import ‘IRanges::shift’ by ‘data.table::shift’ when loading ‘GenomicVis’ 
2: replacing previous import ‘S4Vectors::second’ by ‘data.table::second’ when loading ‘GenomicVis’ 
3: replacing previous import ‘S4Vectors::first’ by ‘data.table::first’ when loading ‘GenomicVis’ 

f2 <- system.file("extdata", "S038_10_wes_S43.vcf", package ="GenomicVis")
f1 <- system.file("extdata", "S038_1_wes_S25.vcf.gz",package = "GenomicVis") vcf.files <- c(f1, f2) sample.names <-c('Sample 1','Sample 10') 
v <- vcf.venn(vcf.files, 'GRCh38', sample.names)

Error in rowData(read.vcf(f, genome, ...)) : could not find function "rowData

But then this Error comes up, no clue how to solve it.

genomicvis • 141 views
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