jmosaics (version 1.12.0)

jmosaics-package: 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

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')