shiny_SNPratio: Shiny SNP-ratio Wrapper Function

In EG-lisy/BSAvis: Bulk Segregant Analysis - Visualisation Package

Description

Please note that this function is not to be run manually. Wrapper function for SNP-ratio plots specific to the R-shiny application. Calls all functions involved in plotting the SNP-ratio values across chromosome positions.

Usage

shiny_SNPratio(
  vcf.list,
  wtBulk,
  mBulk,
  variants,
  min.SNPratio,
  min.DP,
  max.DP,
  chrID,
  chr,
  degree,
  span,
  ranges
)

Arguments

vcf.list	object containing meta information and vcf data frame
wtBulk	Wild-Type pool
mBulk	Mutant pool
variants	variants to be considered. Default is "SNP" (allowed: "SNP" or "all")
min.SNPratio	min value allowed for the SNP index (default=0.3)
min.DP	min value allowed for the read depth (default=50)
max.DP	max value allowed for the read depth (default=200)
chrID	chromosome ID of interest
chr	chromosome name printed on the plot
degree	LOESS smoothing degree (default=2)
span	LOESS smoothing span (default=0.07)
ranges	axes ranges (x,y)

Details

Wrapper function for generting SNP-ratio plots inside the R-Shiny application. The involved functions are the following (in oder): calc_SNPratio(), filter_SNPratio(), extract_chrIDs() and shinyPlot_SNPratio().

This function is not intended to be run by the user, as it was specifically created to be used by the BSAvis_shiny() function.

EG-lisy/BSAvis documentation built on Dec. 17, 2021, 5:38 p.m.