QNB

Version: 1.0

Date: 2016-6-29

Author: Lian Liu liulian19860905@163.com, Jia Meng jia.meng@hotmail.com

Maintainer: Lian Liu liulian19860905@163.com

The package is developed for differential methylation analysis. Estimate variance and mean dependence in count data from MeRIP-seq and test for differential methylation based on a model using quadratic-negative-binomial distribution.

Depends: DESeq

Installation

QNB depends on DESeq and please make sure install them before installing QNB The package can be installed as:

source(“http://bioconductor.org/biocLite.R") biocLite(“DESeq”)

In addtion, R package devtools is required for QNB to be installed from GitHub.

install.packages(“devtools”) At last, QNB can be installed as:

library(“devtools”) install_github(“lianliu09/QNB”) Toy Example

using the data included in the package with replicates

library(QNB)

f1 <- system.file(“extdata”, “meth1.txt”, package=”QNB”)

f2 <- system.file(“extdata”, “meth2.txt”, package=”QNB”)

f3 <- system.file(“extdata”, “unmeth1.txt”, package=”QNB”)

f4 <- system.file(“extdata”, “unmeth2.txt”, package=”QNB”)

meth1 <- read.table(f1,header=TRUE)

meth2 <- read.table(f2,header=TRUE)

unmeth1 <- read.table(f3,header=TRUE)

unmeth2 <- read.table(f4,header=TRUE)

result <- qnbtest(meth1, meth2,unmeth1,unmeth2)

without replicates

f1 <- system.file(“extdata”, “no_rep_meth1.txt”, package=”QNB”)

f2 <- system.file(“extdata”, “no_rep_meth2.txt”, package=”QNB”)

f3 <- system.file(“extdata”, “no_rep_unmeth1.txt”, package=”QNB”)

f4 <- system.file(“extdata”, “no_rep_unmeth2.txt”, package=”QNB”)

no_rep_meth1 <- read.table(f1,header=TRUE)

no_rep_meth2 <- read.table(f2,header=TRUE)

no_rep_unmeth1 <- read.table(f3,header=TRUE)

no_rep_unmeth2 <- read.table(f4,header=TRUE)

result = qnbtest(no_rep_meth1, no_rep_meth2, no_rep_unmeth1, no_rep_unmeth2, mode=”blind”)

mode is auto

result = qnbtest(meth1, meth2,unmeth1,unmeth2,mode=”auto”)