deltaSNPindex_plot: delta(SNP-index) Wrapper Function

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

Description

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

mean_M_SNPindex - mean_WT_SNPindex.WT

Usage

deltaSNPindex_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_deltaSNPindex_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_deltaSNPindex_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 delta(SNP-index) plot: calc_SNPindex(), filter_SNPindex(), extract_chrIDs(), slidingWindow(), calc_deltaSNPindex() and plot_deltaSNPindex(). 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
deltaSNPindex_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
deltaSNPindex_plot(vcf.list=vcf_list, 
              wtBulk="pool_S3781_minus", 
              mBulk="pool_S3781_plus", 
              chrID="SL4.0ch03", 
              chr=3, 
              dpi=1200)
#OR customise default parameters
deltaSNPindex_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="deltaSNPindex_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.