JT.test {SAGx} | R Documentation |
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.
trendA <- JT.test(data = datsA, class = g, labels = c("NS", "HS", "COPD0", "COPD1", "COPD2"))
data |
A matrix with genes in rows and subjects in columns |
class |
the column labels |
labels |
the labels of the categories coded by class |
Assumes that groups are coded in incresing numerical order
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 |
Per Broberg
Lehmann, EH (1975) Nonparametrics: Statistical Methods Based on Ranks p. 233. Holden Day
# 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"))