getTreat-method: Test if coefficient is different from a specified value

In GabrielHoffman/variancePartition: Quantify and interpret drivers of variation in multilevel gene expression experiments

Test if coefficient is different from a specified value

Description

Test if coefficient is different from a specified value

Usage

getTreat(fit, lfc = log2(1.2), coef = 1, number = 10, sort.by = "p")

## S4 method for signature 'MArrayLM'
getTreat(fit, lfc = log2(1.2), coef = 1, number = 10, sort.by = "p")

## S4 method for signature 'MArrayLM2'
getTreat(fit, lfc = log2(1.2), coef = 1, number = 10, sort.by = "p")

Arguments

fit	fit
lfc	a minimum log2-fold-change below which changes not considered scientifically meaningful
coef	which coefficient to test
number	number of genes to return
sort.by	column to sort by

Value

results of getTreat

Examples

data(varPartData)

form <- ~ Age + Batch + (1 | Individual) + (1 | Tissue)

fit <- dream(geneExpr, form, info)
fit <- eBayes(fit)

coef <- "Age"

# Evaluate treat()/topTreat() in a way that works seamlessly for dream()
getTreat(fit, lfc = log2(1.03), coef, sort.by = "none", number = 3)

GabrielHoffman/variancePartition documentation built on Nov. 8, 2024, 11:17 a.m.