plotPedigree: Generate pedigree plots

In vivizhou/MDfilter: Mendelian disease variant filtering

Generate pedigree plots

Description

This function generates pedigree plots to visualize variant information and individual genotypes.

Usage

plotPedigree(
  variant.list,
  pedigree.data,
  includeIDs,
  gene.name = NULL,
  save.path = NULL,
  savePNG = FALSE,
  frequency.col = c("ExAC_All", "X1000G_ALL"),
  label = "test"
)

Arguments

variant.list	Filtered variant list from ?filter.variant()
pedigree.data	Pedigree data load from excel sheet. check ?kinship2::pedigree() for correct format.
includeIDs	IDs of the subjects included for analyses. This must match IDs used in the imported data file.If left empty, IDs will be extracted from the first to the last
gene.name	specify the list of genes in which the variants are to be visualized in the pedigree plots
save.path	Specify save path. If not specified the data will be saved at the working directory.
frequency.col	Column names of the frequencies to be visualized in pedigree plot. For example: frequency.col = c("ExAC_All", "X1000G_ALL", "ExAC_NFE", "X1000G_EUR")
label	Specify the label of the folder to save the files.

Value

Pedigree plot saved as PNG files.

vivizhou/MDfilter documentation built on May 21, 2022, 2:15 a.m.