BAC: Bayesian Analysis of ChIP-chip tiling arrays

Description Usage Arguments Details Value Author(s) See Also Examples

Description

Bayesian Analysis of ChIP-chip tiling arrays

Usage

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BAC(C, I, B=15000,verbose=FALSE,w=5)

Arguments

C

The matrix of control measurements. Rows correspond to probes and columns to samples.

I

The matrix of IP measurements. Rows correspond to probes and columns to samples.

B

Number of iterations used the MCMC. Default to 15000.

verbose

Logical parameter. If TRUE, some progression

w

The window size. Default to 5. See details below for more about this parameter.

Details

The window size should be calculated in function of the resolution and the shearing resolution. For example, for Affymetrix human tiling arrays, the shearing resolution is 500-1000bps, the tiling resolution is 35bps and the probe length is 25bps. Then one would expect a bound region to contain 500-1000/(35+25)~8-16 probes. Thus we decided to set w to 5. Note that the exact value of w is not crucial.

Value

The marginal posterior probabilities and the joint posterior probabilities computed from the Bayesian hierarchical model. We recommend using the joint posterior probabilities to call enriched regions.

Author(s)

Raphael Gottardo, [email protected]

See Also

CallRegions

Examples

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# Load the data
data(ER)
# Only select the first 5000 probes for speed-up
ER<-ER[1:5000,]
# Calculate the joint posterior probabilities
#Only use 100 iterations for speed up (You should use more! See default value) 
BAConER<-BAC(ER[,5:7], ER[,2:4], B=100,verbose=FALSE,w=5)
# For Regions using 0.5 cut-off for the joint posterior probabilities
ERregions<-CallRegions(ER[,1],BAConER$jointPP,cutoff=0.5,maxGap=500)
# Create the BED file
nRegions<-max(ERregions)
BED<-matrix(0,nRegions,4)
for(i in 1:nRegions)
{
BED[i,2:3]<-range(ER[ERregions==i,1])
#The score should be between 0 and 1000
BED[i,4]<-max(BAConER$jointPP[ERregions==i])*1000
}
BED<-data.frame(BED)
# The ER data is a subset of chr 21
BED[,1]<-"chr21"
names(BED)<-c("chrom","chromStart","chromEnd","Score")
# print it
print(BED)

Bioconductor-mirror/BAC documentation built on May 28, 2017, 11:11 p.m.