jmosaics-package: Joint analysis of multiple ChIP-seq data sets

In jmosaics: Joint analysis of multiple ChIP-Seq data sets

Description

Joint analysis of multiple ChIP-seq data sets

Details

Package:	jmosaics
Type:	Package
Version:	1.0
Date:	2012-06-24
License:	GPL(>=2)
LazyLoad:	yes

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

Author(s)

Xin Zeng, Sunduz Keles

Maintainer: Xin Zeng <[e-mail]>

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')

jmosaics documentation built on Oct. 5, 2016, 4:45 a.m.