vjcitn
commented
10 months ago Nice exercise. There is nothing problematic with shiny here, as far as I can tell.
https://gist.github.com/vjcitn/da11ea5228124fd06c5e59239a54cb9d
has edits to your demo code that will run. There are various issues to be addressed -- you don't set the server arguments properly, and you don't call predictCoding with correct arguments.
Keep us posted if you can't make progress on this.
On Fri, Dec 8, 2023 at 2:11 PM FunGeST @.***> wrote:
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$table <-reactive({ renderDT({ if (!is.null(data1())) { datatable(head(data1(), 5)) } }}) } shinyApp(ui = ui, server = server)
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Hi,
We are working on incorporating the readVcf function into our Shiny app, but it appears that Shiny is having trouble recognizing the object format.
After completing the upload, we received an error stating that 'data' must be either a matrix or a data frame and cannot be in the CollapsedVCF format. To address this issue, you may need to coerce the data to a matrix or data frame. Is there any way to collapse the vcf to table that is compatible with shiny?
The same is when trying to use the function predictCoding() Warning: Error in: unable to find an inherited method for function ‘predictCoding’ for signature ‘"CollapsedVCF", "BSgenome", "BSgenome", "missing"’
Many thanks Sandrine
example .. but just for information....
library(shiny) library(dplyr) library(DT) library(VariantAnnotation) library(BSgenome.Hsapiens.UCSC.hg38) txdb <- BSgenome.Hsapiens.UCSC.hg38
ui <- fluidPage( titlePanel("VCF XPLORR"), fileInput("fileInput", "Choose a VCF file", accept = c(".vcf", ".vcf.gz", ".maf"), multiple = FALSE) DTOutput("table") )
server<-function(session, input,output){ options(shiny.maxRequestSize=40*1024^2)
data1 <- reactive({ validate(need(input$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)