JT.test {SAGx}R Documentation

Jonckheere-Terpstra trend test

Description

The test is testing for a monotone trend in terms of the class parameter. The number of times that an individual of a higher class has a higher gene expression forms a basis for the inference.

Usage

trendA <- JT.test(data = datsA, class = g, labels = c("NS", "HS", "COPD0", "COPD1", "COPD2"))

Arguments

data A matrix with genes in rows and subjects in columns
class the column labels
labels the labels of the categories coded by class

Details

Assumes that groups are coded in incresing numerical order

Value

a matrix with the columns

pvalue the p-value for the two-sided test of no trend.
median1 ... mediann the medians for the n groups
trend the rank correlation with category

Author(s)

Per Broberg

References

Lehmann, EH (1975) Nonparametrics: Statistical Methods Based on Ranks p. 233. Holden Day

Examples

# Enter the data as a vector
A <- as.matrix(c(99,114,116,127,146,111, 125,143,148,157,133,139, 149, 160, 184))
# create the class labels
g <- c(rep(1,5),rep(2,5),rep(3,5))
# The groups have the medians
tapply(A, g, median)
# JT.test indicates that this trend is significant at the 5
JT.test(data = t(A), class = g, labels = c("GRP 1", "GRP 2", "GRP 3"))

[Package SAGx version 1.7.1 Index]