DiffChIPL

DiffChIPL: A Differential binding analysis method based on limma for ChIP-seq data featuring biological replicates

Install

1. User can install source package by Rstudio
2. User can also install the package by
3. The dependent packages are as follows: R (>= 4.0.0), tidyverse, broom, limma, edgeR, MASS, GenomicRanges, Rsamtools, bamsignals, readr, SGSeq, roxygen2, RColorBrewer, pracma, readr, dplyr, reshape2, drc, nlme, aomisc,SiZer

library(devtools)
install_github("yancychy/DiffChIPL")

Workflow

Example (simulation)

1. Make a configuration file

The example configuration files are shown in example/simHist/sim_hist_1.csv.

Commonly, the configuration file of DiffBind can be used directly.

2.Get read count from simulated histone datasets

We used the simulation code in csaw to simulate the histone which is a mixture of complex peak structures. We simulated 10000 peaks which have 1000 increased peaks and 1000 decreased peaks. The simulation histone has two groups. In each group, there has two replicates for each histone condition.

library(DiffChIPL)
flib="sim_hist_1.csv"
countL = getReadCount(inputF=flib,overlap=FALSE, fragment=0,
                      removeBackground=TRUE)

3. Make the design matrix and normalization

str1 = "sim-hist1-sim1.vs.sim2-Ridge"
group= c(1,1,0,0)
ctrName = "sim2"
treatName = "sim1"
groupName = c(treatName, treatName,ctrName,ctrName) 
design0 <- cbind(rep(1, 4), c(1,1,0,0))
colnames(design0) <- c(ctrName, treatName)
design0
 
for(i in 1:ncol(countAll)){
  id = which(countAll[,i] < 1)
  countAll[id,i] = 0
}
cpmD = cpmNorm(countAll, libsize = fd$lsIP)

4. Do differential analysis with DiffChIPL

resA = DiffChIPL(cpmD, design0, group0 = group )
fitRlimm3 = resA$fitDiffL
rtRlimm3 = resA$resDE

5. Check the differential results

id_Rlimma_CPM = rownames(rtRlimm3[which(rtRlimm3$adj.P.Val < 0.05),])
 
rtRlimm3 = rtRlimm3[rownames(cpmD),]
aveE = rtRlimm3$AveExpr
logFC = rtRlimm3$logFC
padj = rtRlimm3$adj.P.Val
plotMAVoc2(mean=aveE, logfc=logFC, adj.P.Val=padj, FC=1, 
           refDE= refDE, padj=0.05, MA=TRUE,
          title=paste0("Rlimma-CPM \n", str1,"(padj<0.05)\n", 
                       length(id_Rlimma_CPM), " of ", nrow(rtRlimm3) ))