evalBinSize: Evaluate bin size using Shimazaki cost function

In RIPSeeker: RIPSeeker: a statistical package for identifying protein-associated transcripts from RIP-seq experiments

Description

Given a bin size and a GRanges alignment object, the funciton computes the bin count and returns the cost of the bin size based on Shimazaki cost function.

Usage

evalBinSize(binSize, alignGR)

Arguments

binSize	An integer that indicates the bin size applied to the binning of the chromosome.
alignGR	GRanges object of alignments to a single chromosome.

Details

The function implements the algorithm developed by Shimazaki and Shinomoto (2007), which is based on the goodness of the fit of the time histogram to estimate the rate of neural response of an animal to certain stimuli in a spike-in experiment. The algorithm involves four simple steps:

1. Divide chromosome sequence into N bins of width b.

2. Count number of read counts x_i that enter the i'th bin.

3. Compute: \bar{x} = \frac{1}{N}∑_{i=1}^{N}x_{i} and v = \frac{1}{N}∑_{i=1}^{N}(x_{i} - \bar{x})^{2}.

4. Compute: C(b) = \frac{2\bar{x}-v}{b^{2}}

Value

cost	A scalar value for the cost of the bin size.

Author(s)

Yue Li

References

Hideaki Shimazaki and Shigeru Shinomoto. A method for selecting the bin size of a time histogram. Neural computation, 19(6):1503-1527, June 2007.

See Also

selectBinSize, binCount

Examples

# Retrieve system files
extdata.dir <- system.file("extdata", package="RIPSeeker") 

bamFiles <- list.files(extdata.dir, ".bam$", recursive=TRUE, full.names=TRUE)

bamFiles <- grep("PRC2", bamFiles, value=TRUE)

alignGal <- getAlignGal(bamFiles[1], reverseComplement=TRUE, genomeBuild="mm9")

alignGR <- as(alignGal, "GRanges")

alignGRList <- GRangesList(as.list(split(alignGR, seqnames(alignGR))))

binSize <- 1000

costs <- evalBinSize(binSize, alignGRList$chrX)

RIPSeeker documentation built on Oct. 31, 2019, 7:29 a.m.