Significant SNPs per number of conditions

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.

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

  if (FALSE) mash_plot_sig_by_condition(m = mash_obj, saveoutput = TRUE)