SNPindex_plot: SNP-index Wrapper Function

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

Description

This wrapper function is used to fully run the SNP-index method, by calling all the funcitons involved in plotting the mean SNP-index values from each bulk against the mid position of the corresponding window of a specific chromosome.

SNPindex=AD_alt/(AD_ref + AD_alt)

Usage

SNPindex_plot(
  vcf.list,
  wtBulk,
  mBulk,
  variants = "SNP",
  min.SNPindex = 0.3,
  max.SNPindex = 0.9,
  min.DP = 50,
  max.DP = 200,
  min.GQ = 99,
  chrID,
  chr,
  windowSize = 1e+06,
  windowStep = 10000,
  filename = paste0("plot_SNPindex_ch", chr),
  path = getwd(),
  dpi,
  width = 7.5,
  height = 5,
  units = "in"
)

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)
filename	file name under which the file will be saved (default="plot_SNPindex_chX")
path	path where the file will be saved (default=current working directory)
dpi	resolution value. If no value is given, plots will be generated but not saved
width	width value (default=7.5)
height	height value (default=5)
units	size units (default="in")

Details

Wrapper function that sequentially calls the required functions involved in generating the SNP-index plot: calc_SNPindex(), filter_SNPindex(), extract_chrIDs(), slidingWindow() and plot_SNPindex(). The resulting plot will show (for each bulk) mean SNP-index values against the mid position of the corresponding window of a specific chromosome.

Examples

## Use default values WITHOUT saving the plot
SNPindex_plot(vcf.list=vcf_list, 
         wtBulk="pool_S3781_minus", 
         mBulk="pool_S3781_plus", 
         chrID="SL4.0ch03", 
         chr=3)
## OR use default values AND save the plot
SNPindex_plot(vcf.list=vcf_list, 
         wtBulk="pool_S3781_minus", 
         mBulk="pool_S3781_plus", 
         chrID="SL4.0ch03", 
         chr=3,
         dpi=1200)
#OR customise default parameters
SNPindex_plot(vcf.list=vcf_list, 
         wtBulk="pool_S3781_minus", 
         mBulk="pool_S3781_plus", 
         variants="all",
         min.SNPindex=0.25, 
         max.SNPindex=0.8, 
         min.DP=60, 
         max.DP=250, 
         min.GQ=98,
         chrID="SL4.0ch03", 
         chr=3,
         windowSize=2000000, 
         windowStep=20000,
         filename="SNPindex_chrom03", 
         path="Document/Plots", 
         dpi=1200,
         width=20, 
         height=12, 
         units="cm")

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