get.sig.snps: Get significant SNPs, according to a given test of...

In caitiecollins/treeWAS: Phylogenetic tree-based microbial GWAS

Get significant SNPs, according to a given test of association.

Description

Identify which SNPs are deemed to be significantly associated with a phenotype, according to a given test of association and p-value. (Serves as the treeWAS association testing function; runs the assoc.test function internally.)

Usage

get.sig.snps(
  corr.dat,
  corr.sim,
  snps.names,
  test = "terminal",
  p.value = 0.01,
  p.value.correct = "bonf",
  p.value.by = "count"
)

Arguments

corr.dat	A vector containing the association score values, for a given association test, for the real data.
corr.sim	A vector containing the association score values, for a given association test, for the simulated data.
snps.names	The column names of the original snps matrix from which the association score values in corr.dat were derived.
test	A character string or vector containing one or more of the following available tests of association: "terminal", "simultaneous", "subsequent", "cor", "fisher". By default, the terminal test is run (note that within treeWAS, the first three tests are run in a loop by default). See details for more information on what these tests do and when they may be appropriate.
p.value	A single number specifying the p.value below which correlations are deemed to be 'significant'.
p.value.correct	Specify if/how to correct for multiple testing: either FALSE, or one of 'bonf' or 'fdr' (indicating, respectively, the Bonferroni and False Discovery Rate corrections). By default, 'bonf' is selected
p.value.by	Specify how to determine the location of the p.value threshold: either 'count' or 'density' (indicating, respectively, that the p.value threshold should be determined by exact count or with the use of a density function).

Author(s)

Caitlin Collins [e-mail]

caitiecollins/treeWAS documentation built on March 9, 2024, 3:15 p.m.