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

# S4 method for 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)
#>             logFC     AveExpr t   P.Value adj.P.Val         B z.std
#> gene1 0.005551165 -10.4664549 0 0.9883098 0.9997873 -6.323909     0
#> gene2 0.013121135  -1.1281610 0 0.9586897 0.9997873 -6.085180     0
#> gene3 0.020151496   0.1702122 0 0.9212652 0.9997873 -5.585951     0