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README.md

MeTPeak

Version: 1.1

Date: 2016-2-2

Author: Xiaodong Cui xiaodong.cui@outlook.com, Jia Meng jia.meng@hotmail.com

Maintainer: Xiaodong Cui xiaodong.cui@outlook.com

The package is developed for the finding the location of m6A sites in MeRIP-seq data

License: GPL-2

Depends: Rsamtools, GenomicFeatures (>= 1.0.0), rtracklayer, BH, RcppArmadillo, Rcpp

Installation

R package devtools is required for metpeak to be installed from GitHub.

install.packages("devtools")

Some of MeTPeak dependent packages have to be installed from BiocLite, At last, MeTPeak can be installed as:

library("devtools")
source("https://bioconductor.org/biocLite.R")
install_github("compgenomics/MeTPeak",build_opts = c("--no-resave-data", "--no-manual"))

Toy Example

# using the data included in the package
library(MeTPeak)

# in the real case, change the gtf to what you need
gtf <- system.file('extdata','example.gtf',package='MeTPeak')

ip1 <- system.file('extdata','IP1.bam',package='MeTPeak')
ip2 <- system.file('extdata','IP2.bam',package='MeTPeak')
ip3 <- system.file('extdata','IP3.bam',package='MeTPeak')
input1 <- system.file('extdata','Input1.bam',package='MeTPeak')
input2 <- system.file('extdata','Input2.bam',package='MeTPeak')
input3 <- system.file('extdata','Input3.bam',package='MeTPeak')

IP_BAM <- c(ip1,ip2,ip3)
INPUT_BAM <- c(input1,input2,input3)

metpeak(GENE_ANNO_GTF=gtf,IP_BAM = IP_BAM,INPUT_BAM = INPUT_BAM,
        EXPERIMENT_NAME="example")

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