analysis/ChIP analysis/DiffBind on ChIPseq.R

In a3609640/panda: Analyze RNA Sequencing Data

source("https://bioconductor.org/biocLite.R")

# install the dependent files for DiffBind
biocLite("GenomicFeatures")
biocLite("GenomicRanges")
biocLite("SummarizedExperiment")
biocLite("VariantAnnotation")
biocLite("RMySQL")
biocLite("systemPipeR")
biocLite("codetools")
biocLite("DiffBind")

library(GenomicFeatures)
library(GenomicRanges)
library(SummarizedExperiment)
library(VariantAnnotation)
library(RMySQL)
library(systemPipeR)
library(codetools)
library(lattice)
library(Matrix)
library(spatial)
library(DiffBind)
# setwd(system.file("extra", package="DiffBind"))
setwd("~/Documents/Bioinformatics analysis/ChIP analysis/A549-SREBP1")

# examples <- read.csv("tamoxifen.csv")
# names(examples)
samples <- read.csv("Diffbinddata.csv")
names(samples)
tamoxifen <- dba(sampleSheet="Diffbinddata.csv")

tamoxifen <- dba.count(tamoxifen)
plot(tamoxifen) 
tamoxifen <- dba.contrast(tamoxifen)
plot(tamoxifen) 
tamoxifen <- dba.analyze(tamoxifen)
plot(tamoxifen, contrast=1)
tamoxifen.DB <- dba.report(tamoxifen)
corvals <- dba.plotHeatmap(tamoxifen)


samples <- read.csv(file.path(system.file("extra", package="DiffBind"),"tamoxifen.csv"))
names(samples)
tamoxifen <- dba(sampleSheet="tamoxifen.csv")
tamoxifen
plot(tamoxifen)