limma_a_b: Wrapper for Limma

Description Usage Arguments Value Functions Note Examples

View source: R/limma_a_b.R

Description

A convenience wrapper for limma

Usage

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limma_a_b(eset, model.str, coef.str, ...)

limma_gen(eset, model.str, coef.str, ...)

Arguments

eset

eset (or most likely eset subclass) object

model.str

character formulation of the model (e.g. "~ a + b")

coef.str

character coefficient of interest. E.g. "a". Either numeric or factor with 2 levels.

...

arguments for lmFit

Value

data.frame. Basically output of topTable function.

Functions

Note

limma_a_b is for either 2-factor ANOVA or linear regression. limma_gen is a more generic version and will return results for all the coefficients that match coef.str pattern.

Examples

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library("vp.misc")
data("cptac_oca")
library("limma")
ee <- oca.set
ee <- ee[rowSums(!is.na(exprs(ee))) >= 30,]
model.string <- "~ PLATINUM.STATUS + AGE" # model with covariates
coef.string <- "PLATINUM.STATUS" # note, only two levels allowed here

res <- limma_a_b(oca.set, 
                 model.str = "~ PLATINUM.STATUS + AGE", 
                 coef.str = "PLATINUM.STATUS")
head(res)

vladpetyuk/vp.misc documentation built on June 25, 2021, 6:35 a.m.