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
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"))
# 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")