In slzhao/mafreport:

Summary Tables

Overall Summary

kable(dataForReport[["maf"]]@summary)

Silent Variants Summary (Removed)

if ("vc_nonSyn" %in% names(dataForReport)) {
  kable(summarySilentMaf(dataForReport[["maf"]]@maf.silent,vc.nonSilent=dataForReport[["vc_nonSyn"]]))
} else {
  kable(summarySilentMaf(dataForReport[["maf"]]@maf.silent))
}

Variants Classification

#gvisTable(dataForReport[["maf"]]@variant.classification.summary,options=tableVisOptions)
makeDataTable(dataForReport[["maf"]]@variant.classification.summary)

Variants Type

#gvisTable(dataForReport[["maf"]]@variant.type.summary,options=tableVisOptions)
makeDataTable(dataForReport[["maf"]]@variant.type.summary)

High Prevelance Variants

#makeDataTable(summaryVariant(dataForReport[["maf"]],vIdCol=dataForReport[["vIdCol"]])[1:200,])
makeDataTable(dataForReport[["mafProcessed"]]$variantCountSummary[1:200,])

Variants Per Gene

#gvisTable(dataForReport[["maf"]]@gene.summary,options=tableVisOptions)
makeDataTable(dataForReport[["maf"]]@gene.summary)

slzhao/mafreport documentation built on April 29, 2023, 8:39 a.m.