readVcf(), VariantAnnotation and shiny compatibility

まず、示されている BSgenome オブジェクトを使い、readVcf()、subset()、predictCoding() で提供された Shiny の例を再現します。CollapsedVCF の結果が DT と predictCoding() にどのように渡されるかを調べ、それらのシグネチャで利用可能なメソッドを確認します。互換性の問題と、サポートされている変換または使用の経路が明確に確立されれば完了です。

Hi,

We are working on incorporating the readVcf function into our Shiny app, but it appears that Shiny is having trouble recognizing the object format.

After completing the upload, we received an error stating that 'data' must be either a matrix or a data frame and cannot be in the CollapsedVCF format. To address this issue, you may need to coerce the data to a matrix or data frame.
Is there any way to collapse the vcf to table that is compatible with shiny?

The same is when trying to use the function predictCoding()
Warning: Error in : unable to find an inherited method for function ‘predictCoding’ for signature ‘"CollapsedVCF", "BSgenome", "BSgenome", "missing"’

Many thanks
Sandrine

example .. but just for information....

library(shiny)
library(dplyr)
library(DT)
library(VariantAnnotation)
library(BSgenome.Hsapiens.UCSC.hg38)
txdb <- BSgenome.Hsapiens.UCSC.hg38

ui <- fluidPage(
titlePanel("VCF XPLORR"),
fileInput("fileInput", "Choose a VCF file", accept = c(".vcf", ".vcf.gz", ".maf"),
multiple = FALSE)
DTOutput("table")
)

server<-function(session, input,output){
options(shiny.maxRequestSize=40*1024^2)

data1 <- reactive({
validate(need(input$fileInput,""))
if (is.null(input$fileInput)) {
return(NULL)
} else {
raw_vcf_data <- readVcf(input$fileInput$datapath, 'hg38')

Perform filtering based on the FILTER column

filtered_vcf_data <- subset(raw_vcf_data, FILTER == "PASS")
coding <- predictCoding(filtered_vcf_data, txdb, seqSource=Hsapiens) %>%
as.data.frame()

return(coding)

})

output$table <-reactive({ renderDT({
if (!is.null(data1())) {
datatable(head(data1(), 5))
}
}})
}
shinyApp(ui = ui, server = server)