Joint analysis of multiple ChIP-seq data sets

Description

Joint analysis of multiple ChIP-seq data sets

Details

readBinsMultiple match coordinates for multiple datasets,jmosaicsPattern call E_LAYER and B_LAYER peaks

Author(s)

Xin Zeng, Sunduz Keles

Maintainer: Xin Zeng <xinzeng@stat.wisc.edu>

References

jMOSAiCS: Joint Analysis of Multiple ChIP-seq Datasets

Examples

## step by step not run
## Not run: 
bin1 <- readBins(type = c("chip", "M", "GC", "N","input"), 
 fileName = c("h3k27me3_chip_chr10.txt",
 "./M_chr10.txt", "./GC_chr10.txt", "./N_chr10.txt",
"h3k27me3_input_chr10.txt"))
bin2 <- readBins(type = c("chip", "M", "GC", "N","input"), 
 fileName = c("h3k4me1_chip_chr10.txt",
 "./M_chr1.txt", "./GC_chr10.txt", "./N_chr10.txt",
 "h3k4me1_input_chr10.txt"))
origin_bin <- list(bin1, bin2)

## End(Not run)

data("jmosaics_example_data")
bin <- readBinsMultiple(origin_bin)
fit1 <- mosaicsFit(bin[[1]], analysisType = "IO")
fit2 <- mosaicsFit(bin[[2]], analysisType = "IO")
fit <- list(fit1,fit2)
result <- jmosaicsPattern(fit, region_length=1, FDR=0.01, thres=c(10,10), type=c('B','E','Pattern'), patternInfo='FALSE')

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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Type 'demo()' for some demos, 'help()' for on-line help, or
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> library(jmosaics)
Loading required package: mosaics
Loading required package: Rcpp
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/jmosaics/jmosaics-package.Rd_%03d_medium.png", width=480, height=480)
> ### Name: jmosaics-package
> ### Title: Joint analysis of multiple ChIP-seq data sets
> ### Aliases: jmosaics-package jmosaics
> 
> ### ** Examples
> 
> 
> ## step by step not run
> ## Not run: 
> ##D bin1 <- readBins(type = c("chip", "M", "GC", "N","input"), 
> ##D  fileName = c("h3k27me3_chip_chr10.txt",
> ##D  "./M_chr10.txt", "./GC_chr10.txt", "./N_chr10.txt",
> ##D "h3k27me3_input_chr10.txt"))
> ##D bin2 <- readBins(type = c("chip", "M", "GC", "N","input"), 
> ##D  fileName = c("h3k4me1_chip_chr10.txt",
> ##D  "./M_chr1.txt", "./GC_chr10.txt", "./N_chr10.txt",
> ##D  "h3k4me1_input_chr10.txt"))
> ##D origin_bin <- list(bin1, bin2)
> ## End(Not run)
> 
> data("jmosaics_example_data")
> bin <- readBinsMultiple(origin_bin)
> fit1 <- mosaicsFit(bin[[1]], analysisType = "IO")
Info: background estimation based on robust method of moment.
Info: two-sample analysis (Input only).
Info: use adaptive griding.
Info: fitting background model...
Info: done!
Info: fitting one-signal-component model...
Info: fitting two-signal-component model...
Info: calculating BIC of fitted models...
Error in initialize(value, ...) : 
  no slot of name "seqDepth" for this object of class "BinData"
Calls: mosaicsFit ... .local -> .mosaicsFit_IO -> new -> initialize -> initialize
Execution halted