getPval: Get p-value

In ramellose/CoNetinR: CoNet implementation in R

Description

Get permuation-based p-value for association between two vectors.

Usage

getPval(matrix, x.index, y.index, N.rand = 1000, method = "spearman",
  renorm = F, permutandboot = F, plot = F, verbose = F)

Arguments

matrix	input matrix
x.index	index of first vector in the input matrix
y.index	index of second vector in the input matrix
N.rand	number of iterations used for the permutation test
method	similarity measure (supported measures are: "pearson", "spearman", "bray" and "kld")
renorm	renormalize after permutation
permutandboot	compute a bootstrap distribution in addition to the permutation distribution and
plot	plot the histogram of the permutation and, if permutandboot is true, of the bootstrap distribution
verbose	print distribution properties and p-value

Details

# Compute the association between two vectors using the given method and compute its p-value using a permutation test. This method was adapted from R code by Fah Sahtirapongsasuti. This method was adapted from CCREPE: http://huttenhower.sph.harvard.edu/ccrepe. Emma Schwager et al Detecting statistically significant associtations between sparse and high dimensional compositional data. (In progress).

Value

p-value of the association

ramellose/CoNetinR documentation built on Oct. 16, 2019, 9:50 a.m.