mash_plot_sig_by_condition: Significant SNPs per number of conditions

In Alice-MacQueen/CDBNgenomics: Genomics Using the Cooperative Dry Bean Nursery Dataset

Description

For some number of columns in a mash object that correspond to conditions, find the number of SNPs that are significant for that number of conditions.

Usage

mash_plot_sig_by_condition(
  m,
  conditions = NA,
  saveoutput = FALSE,
  suffix = "",
  thresh = 0.05
)

Arguments

m	An object of type mash
conditions	A vector of conditions. Get these with get_colnames(m).
saveoutput	Logical. Save plot output to a file? Default is FALSE.
suffix	Character. Optional. A unique suffix used to save the files, instead of the current date & time.
thresh	What is the threshold to call an effect significant? Default is 0.05.

Value

A list containing a dataframe of the number of SNPs significant per number of conditions, and a ggplot object using that dataframe.

Examples

  ## Not run: mash_plot_sig_by_condition(m = mash_obj, saveoutput = TRUE)

Alice-MacQueen/CDBNgenomics documentation built on Aug. 18, 2020, 4:39 p.m.