inst/doc/RareVariantsVis.R

In RareVariantVis: A suite for analysis of rare genomic variants in whole genome sequencing data

## ----mychunk1, cache=TRUE, eval=FALSE, hide=TRUE------------------------------
#  library(RareVariantVis)
#  library(DataRareVariantVis)

## ----mychunk2, cache=TRUE, eval=FALSE, hide=TRUE------------------------------
#  sample = system.file("extdata", "CoriellIndex_S1.vcf.gz",
#      package = "DataRareVariantVis")
#  sv_sample = system.file("extdata", "CoriellIndex_S1.sv.vcf.gz",
#      package = "DataRareVariantVis")

## ----mychunk3, cache=TRUE, eval=FALSE, hide=TRUE------------------------------
#  chromosomeVis(sample=sample, sv_sample=sv_sample,
#      chromosomes=c("19"))

## ----mychunk4, cache=TRUE, eval=FALSE, hide=TRUE------------------------------
#  rareVariantVis("RareVariants_CoriellIndex_S1.txt",
#                 "RareVariants_CoriellIndex_S1.html",
#                 "CorielIndex")

## ----mychunk5, cache=TRUE, eval=FALSE, hide=TRUE------------------------------
#  inputFiles = c("RareVariants_CoriellIndex_S1.txt",
#                 "RareVariants_Coriell_S2.txt")
#  sampleNames = c("CoriellIndex_S1", "Coriell_S2");
#  multipleVis(inputFiles, "CorielSamples.html", sampleNames, "19")