Local z-score

Description

Evaluates tthe variation of the z-score in the vicinty of the original region set

Usage

localZScore(A, pt, window, step, ...)

Arguments

Value

It returns a local z-score object

See Also

overlapPermTest, permTest

Examples

genome <- filterChromosomes(getGenome("hg19"), keep.chr="chr1")
A <- createRandomRegions(nregions=20, length.mean=10000, length.sd=20000, genome=genome, non.overlapping=FALSE) 
B <- c(A, createRandomRegions(nregions=10, length.mean=10000, length.sd=20000, genome=genome, non.overlapping=FALSE))

pt <- overlapPermTest(A=A, B=B, ntimes=10, genome=genome, non.overlapping=FALSE)
plot(pt)
 
lz <- localZScore(A=A, B=B, pt=pt)
plot(lz)


pt2 <- permTest(A=A, B=B, ntimes=10, randomize.function=randomizeRegions, evaluate.function=list(overlap=numOverlaps, distance=meanDistance), genome=genome, non.overlapping=FALSE)
plot(pt2)

lz2 <- localZScore(A=A, B=B, pt2)
plot(lz2)

 

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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> library(regioneR)
Loading required package: memoise
Loading required package: GenomicRanges
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: BSgenome
Loading required package: Biostrings
Loading required package: XVector
Loading required package: rtracklayer
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/regioneR/localZScore.Rd_%03d_medium.png", width=480, height=480)
> ### Name: localZScore
> ### Title: Local z-score
> ### Aliases: localZScore
> 
> ### ** Examples
> 
> 
> genome <- filterChromosomes(getGenome("hg19"), keep.chr="chr1")
> A <- createRandomRegions(nregions=20, length.mean=10000, length.sd=20000, genome=genome, non.overlapping=FALSE) 
> B <- c(A, createRandomRegions(nregions=10, length.mean=10000, length.sd=20000, genome=genome, non.overlapping=FALSE))
> 
> pt <- overlapPermTest(A=A, B=B, ntimes=10, genome=genome, non.overlapping=FALSE)
[1] "Note: The minimum p-value with only 10 permutations is 0.0909090909090909. You should consider increasing the number of permutations."
> plot(pt)
>  
> lz <- localZScore(A=A, B=B, pt=pt)
> plot(lz)
> 
> 
> pt2 <- permTest(A=A, B=B, ntimes=10, randomize.function=randomizeRegions, evaluate.function=list(overlap=numOverlaps, distance=meanDistance), genome=genome, non.overlapping=FALSE)
[1] "Note: The minimum p-value with only 10 permutations is 0.0909090909090909. You should consider increasing the number of permutations."
Warning message:
In permTest(A = A, B = B, ntimes = 10, randomize.function = randomizeRegions,  :
  All permuted values are equal to 0. Z-score is infinite.
> plot(pt2)
Warning message:
In plot.permTestResults(X[[i]], ...) :
  all permuted values are equal to 0. It is not posible to adjust a normal distribution nor to compute a Z-score.
> 
> lz2 <- localZScore(A=A, B=B, pt2)
> plot(lz2)
Error in plot.window(...) : need finite 'ylim' values
Calls: plot ... plot.localZScoreResults -> plot -> plot.default -> localWindow -> plot.window
Execution halted