The goal of rmRNAseq is to conduct differential expression analysis using RNA-seq data from repeated-measures designs, where mRNA samples are obtained repeatedly at different times from same experimental units. Our method is developed based on a general linear model framework with continuous autoregressive correlation structure of order one, accompanied by a parametric bootstrap inference strategy to conduct general hypothesis testings.
You can install the released version of rmRNAseq from CRAN with:
install.packages("rmRNAseq")
(The package has just been submitted to CRAN on June 26, 2019; it usually takes about 10 days to receive their feedback.)
And the development version from GitHub with:
# install.packages("devtools")
devtools::install_github("ntyet/rmRNAseq")
This is a basic example which shows you how to solve a common problem:
library(rmRNAseq)
data(dat)
data(design)
data(covset)
Subject <- covset$ear # identity of experimental units
Time <- covset$time # times at which mRNA samples are taken
Nboot <- 2 # for real data analysis, use Nboot at least 100
ncores <- 1 # for real data analysis and if the computer allows, increase ncores to save time
print.progress <- FALSE
saveboot <- FALSE
counts <- dat[1:3,]
C.matrix <- list()
# test for Line main effect
C.matrix[[1]] <- limma::makeContrasts(line2, levels = design)
# test for Time main effect
C.matrix[[2]] <- limma::makeContrasts(time2, time6, time24, levels = design)
names(C.matrix) <- c("line2", "time")
TCout <- rmRNAseq:::TC_CAR1(counts, design, Subject, Time, C.matrix,
Nboot, ncores, print.progress, saveboot)
#> running bootstrap sample nrep = 1
#> ---------------------------------------------
#> running bootstrap sample nrep = 2
#> ---------------------------------------------
names(TCout)
#> [1] "NewTime" "TimeMinOut" "ori.res" "pqvalue"
TCout$NewTime[1:4]
#> [1] 0.1492027 0.8028973 1.0000000 0.0000000
TCout$pqvalue$pv
#> line2 time
#> 1 0.2857143 0.1428571
#> 2 0.1428571 0.1428571
#> 3 1.0000000 0.1428571
TCout$pqvalue$qv
#> line2 time
#> 1 0.4285714 0.1428571
#> 2 0.4285714 0.1428571
#> 3 1.0000000 0.1428571
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.