myTopTags: Top Tags from edgeR analysis

In floatofmath/bt88.03.704: floats MSI utility function

Top Tags from edgeR analysis

Description

Makes a nice table from edger test results

Usage

myTopTags(lrts, N = NULL, annodata = NULL, key = "nearest_ref_id")

Arguments

lrts	DGELRT object
N	number of tags to display (if not set will show all values with FDR adjusted p-value below 0.05)
annodata	a data.table object with additionall annotation data
key	index variable shared with annotation data

Value

a data.table with the top expressed tags

Author(s)

Florian Klinglmueller

Examples

## setting up some random data
data <- matrix(rpois(600,200),ncol=6)
dge <- DGEList(counts=data)
dge <- estimateDisp(dge)

## a design matrix
design <- data.frame('Treatment' = factor(rep(0:1,each=3)))
mm <- model.matrix(~0+Treatment,design)

## a contrast matrix
colnames(mm) <- c('control','treatment')
cm <- makeContrasts('control-treatment',levels=mm)

## fit and test
out <- fit.edger(dge,mm,cm)

myTopTags(out,3)

floatofmath/bt88.03.704 documentation built on March 25, 2022, 12:28 p.m.