BinData-class: Class "BinData"

In dongjunchung/mosaics: MOSAiCS (MOdel-based one and two Sample Analysis and Inference for ChIP-Seq)

Description

This class represents bin-level ChIP-seq data.

Objects from the Class

Objects can be created by calls of the form new("BinData", ...).

Slots

chrID:

Object of class "character", a vector of chromosome IDs.

coord:

Object of class "numeric", a vector of genomic coordinates.

tagCount:

Object of class "numeric", a vector of tag counts of ChIP sample.

mappability:

Object of class "numeric", a vector of mappability score.

gcContent:

Object of class "numeric", a vector of GC content score.

input:

Object of class "numeric", a vector of tag counts of matched control sample.

dataType:

Object of class "character", indicating how reads were processed. Possible values are "unique" (only uniquely aligned reads were retained) and "multi" (reads aligned to multiple locations were also retained).

seqDepth:

Object of class "numeric", a vector of sequencing depth of length 2, where the first and second elements correpond to sequencing depths of ChIP and control samples, respectively. If there is not control sample, the second element is set to NA.

Methods

mosaicsFit

signature(object = "BinData"): fit a MOSAiCS model using a bin-level ChIP-seq data.

plot

signature(x = "BinData", y = "missing", plotType = NULL ): provide exploratory plots of mean ChIP tag counts. This method plots mean ChIP tag counts versus mappability score, GC content score, and Control tag counts, with 95% confidence intervals, for plotType="M", plotType="GC", and plotType="input", respectively. plotType="M|input" and plotType="GC|input" provide plots of mean ChIP tag counts versus mappability and GC content score, respectively, conditional on Control tag counts. If plotType is not specified, this method plots histogram of ChIP tag counts.

print

signature(x = "BinData"): return bin-level data in data frame format.

show

signature(object = "BinData"): provide brief summary of the object.

chrID

signature(object = "BinData"): provide a vector of chromosome ID.

coord

signature(object = "BinData"): provide a vector of genomic coordinates.

tagCount

signature(object = "BinData"): provide a vector of tag count of ChIP sample.

input

signature(object = "BinData"): provide a vector of tag count of input sample.

mappability

signature(object = "BinData"): provide a vector of mappability score.

gcContent

signature(object = "BinData"): provide a vector of GC content score.

seqDepth

signature(object = "BinData"): provide a vector of sequencing depth.

Author(s)

Dongjun Chung, Pei Fen Kuan, Rene Welch, Sunduz Keles

References

Kuan, PF, D Chung, G Pan, JA Thomson, R Stewart, and S Keles (2011), "A Statistical Framework for the Analysis of ChIP-Seq Data", Journal of the American Statistical Association, Vol. 106, pp. 891-903.

Chung, D, Zhang Q, and Keles S (2014), "MOSAiCS-HMM: A model-based approach for detecting regions of histone modifications from ChIP-seq data", Datta S and Nettleton D (eds.), Statistical Analysis of Next Generation Sequencing Data, Springer.

See Also

readBins, mosaicsFit.

Examples

showClass("BinData")
## Not run: 
library(mosaicsExample)
data(exampleBinData)

exampleBinData
print(exampleBinData)[1:10,]
plot(exampleBinData)
plot( exampleBinData, plotType="M" )
plot( exampleBinData, plotType="GC" )
plot( exampleBinData, plotType="input" )
plot( exampleBinData, plotType="M|input" )
plot( exampleBinData, plotType="GC|input" )

exampleFit <- mosaicsFit( exampleBinData, analysisType="IO" )

## End(Not run)

dongjunchung/mosaics documentation built on March 1, 2020, 3:44 a.m.