Isofudge {IsoGene} | R Documentation |
The function calculates the fudge factor for SAM test statistics for the five test statistics (the global likelihood test, Williams, Marcus, M, and the modified M).
Isofudge(x, y)
x |
indicates the dose levels |
y |
gene expression for all genes |
A vector of five fudge factor values for the five SAM test statistics.
This function calculates the fudge factor for SAM test statistics for the five test statistics.
Lin et al.
isoreg
, Isoallfdr
, IsoGenemSAM
, Isoqqstat
,
Isoqval
,IsoTestSAM
,IsoSAMPlot
set.seed(1234) x <- c(rep(1,3),rep(2,3),rep(3,3)) y1 <- matrix(rnorm(4500, 1,1),500,9) ## 500 genes with no trends y2 <- matrix(c(rnorm(1500, 1,1),rnorm(1500,2,1),rnorm(1500,3,1)),500,9) ## 500 genes with increasing trends y <- data.frame(rbind(y1, y2)) ##y needs to be a data frame fudge.factor <- Isofudge(x,y)