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

# S4 method for class '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 0.9882946 0.9997854 -6.323485     0
#> gene2 0.013121135  -1.1281610 0 0.9586703 0.9997854 -6.084858     0
#> gene3 0.020151494   0.1702122 0 0.9211006 0.9997854 -5.586873     0