shiny_deltaSNPindex: delta(SNP-index) 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 delta(SNP-index) plots specific to the R-shiny application. Calls all functions involved in plotting delta(SNP-index) values against the mid position of the corresponding window of a specific chromosome.

Usage

shiny_deltaSNPindex(
  vcf.list,
  wtBulk,
  mBulk,
  variants = "SNP",
  min.SNPindex,
  max.SNPindex,
  min.DP,
  max.DP,
  min.GQ,
  chrID,
  chr,
  windowSize,
  windowStep,
  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.SNPindex	min value allowed for the SNP index (default=0.3)
max.SNPindex	max value allowed for the SNP index (default=0.9)
min.DP	min value allowed for the read depth (default=50)
max.DP	max value allowed for the read depth (default=200)
min.GQ	min value allowed for the genotype quality (default=99)
chrID	chromosome ID of interest
chr	chromosome name printed on the plot
windowSize	window size (default=1000000)
windowStep	window step (default=10000)
ranges	axes ranges (x,y)

Details

Wrapper function for generting delta(SNP-index) plots inside the R-Shiny application. The involved functions are the following (in oder): calc_SNPindex(), filter_SNPindex(), extract_chrIDs(), slidingWindow() and shinyPlot_SNPindex().

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.