regioner an r/bioconductor package for the magement and comparision of genomic regions anna díez...

regioneRan R/Bioconductor package for the magement and comparision of genomic regions

Anna DíezBernat GelRoberto Malinverni

regioneR aimsPractical to use. Easy to understand.

Generic and useful

Efficient

Customizable Something we would like to use

regioneRBasic management of genomic regions

Statistical evaluation

Helper function making our lives easier

The BasicsStatistics

Customization

Helper Functions

The Basics Statistics Customization Helper Functions


THE BASICS

joinRegions


Amin.dist

joinRegions(A, min.dist)

subtractRegions


A

B

subtractRegions(A, B)

splitRegions


A

B

splitRegions(A, B, min.size=1, track.original=TRUE)

mergeRegions


commonRegions

extendRegions¿any other? flankingRegions? …

overlapRegions


A

B

overlapRegions(A, B, colA, colB, type, min.bases, min.pctA, min.pctB, get.pctA, get.pctB, get.bases, only.boolean, only.count, ...)

overlapRegions


Example: annotateRegions


regAnnotation(regions, annot.tab, ann.names, strands, descr, peak.point, gap3,

gap5)


STATISTICS

overlapPermTest


A

BB

overlapPermTest


A

B

B’4

4

3

5

4

5

2

4

0.33

1

overlapPermTest


Example: TIs


TIs over: 81TIs under 66

SCNA gain: 60SCNA losses: 53


Number of permutations: 1000Alternative: greaterEvaluation of the original region set: 81Summary of the evaluation of the permuted region set: Min. 1st Qu. Median Mean 3rd Qu. Max. 37.00 47.00 50.00 50.43 53.00 67.00 Standard score: 6.8117P-value: 0.000999000999000999 ***--- Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

overlapPermTest(TIs_over, SCNA.gains, alternative="g“, genome=“hg19”, ntimes=1000)

Gains vs Overexpression

~800s (~13min)


Number of permutations: 1000Alternative: greaterEvaluation of the original region set: 66Summary of the evaluation of the permuted region set: Min. 1st Qu. Median Mean 3rd Qu. Max. 37.00 48.00 50.00 50.18 53.00 60.00 Standard score: 4.4942P-value: 0.000999000999000999 ***--- Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

overlapPermTest(Tis_under, SCNA.losses, alternative="g“, genome=“hg19”, ntimes=1000)

Losses vs Underexpression


Number of permutations: 1000Alternative: greaterEvaluation of the original region set: 25Summary of the evaluation of the permuted region set: Min. 1st Qu. Median Mean 3rd Qu. Max. 30.00 39.00 41.00 41.25 44.00 52.00 Standard score: -4.2739P-value: 1 --- Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

overlapPermTest(TIs_under, SCNA.gains, alternative="g“, genome=“hg19”, ntimes=1000)

Gains vs Underexpression

recomputePermTest(gains.under, alternative="l")


Number of permutations: 1000Alternative: lessEvaluation of the original region set: 25Summary of the evaluation of the permuted region set: Min. 1st Qu. Median Mean 3rd Qu. Max. 30.00 39.00 41.00 41.25 44.00 52.00 Standard score: -4.2739P-value: 0.000999000999000999 ***

overlapPermTest(TIs_under, SCNA.gains, alternative=“l“, genome=“hg19”, ntimes=1000)

Gains vs Underexpression


overlapPermTest(10KrandomA, 10KrandomB, alternative=“g“, genome=“hg19”, ntimes=1000)

Random Region Sets

Number of permutations: 1000Alternative: greaterEvaluation of the original region set: 68Summary of the evaluation of the permuted region set: Min. 1st Qu. Median Mean 3rd Qu. Max. 42.00 57.00 62.00 62.16 67.00 89.00 Standard score: 0.7488P-value: 0.215784215784216 --- Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

~1850s (~30min) (Single core)

~800s (~13min) (Parallel 4 cores)

permTest


overlapPermTestoverlap

randomRegions

distance

resampling

value of a function

permTest


permTest(A, ntimes=1000, randomize.function, evaluate.function, alternative, min.parallel=1000, force.parallel=NULL, ...)

overlapPermTest <- permTest(A, randomize.function=randomizeRegions, evaluate.function=countOverlaps)

Example: Genes & ALUs


1.175.329 ALUs 9.111 overexpressed genes51.796 genes

¿Are overexpressed genes closer to ALUs than expected by chance?



Resampling


Mean Distance

permTest(A=expressed, B=alus, ntimes=1000, randomize.function=resampleRegions, universe=genes2, evaluate.function=meanDistance, alternative="less")




Number of permutations: 1000 Alternative: less Evaluation of the original region set: 353.371858193393 Summary of the evaluation of the permuted region set: Min. 1st Qu. Median Mean 3rd Qu. Max. 912.1 992.8 1010.0 1011.0 1028.0 1095.0 Standard score: -25.0275 P-value: 0.000999000999000999 ***


CUSTOMIZATION


countOverlapsmeanDistancemeanInRegions

Available functions

randomizeRegionsresampleRegions

Evaluation Randomization

GC content TF binding sites Encode classification …

GC aware randomization …


Custom functions

randomize.function(A,...)

Randomization

resampleRegions <- function(A, universe, ...) { resample <- universe[sample(1:length(universe), length(A))] return(resample) }


Custom functions

evaluate.function(A,...)

Evaluation

meanDistance <- function(A, B, ...) {d <- distanceToNearest(A, B, ...)

return(mean(as.matrix(d@elementMetadata)[,1])) }


HELPERFUNCTIONS


toGRanges & toDataframe

chr start end chr1 2000 4000 chr1 5000 5500 chr1 10000 12000

GRanges with 3 ranges and 0 elementMetadata values seqnames ranges strand | <Rle> <IRanges> <Rle> | [1] chr1 [ 2000, 4000] * | [2] chr1 [ 5000, 5500] * | [3] chr1 [10000, 12000] * |

Seqlengths chr1 NA


Genomes & MasksgetGenome(genome)

getMask(genome)

getGenomeAndMask(genome, mask)

characterToBSGenome(genome.id)

maskFromBSGenome(bsgenome)

emptyCache()


RandomizationrandomizeRegions(A, genome="hg19", mask=NULL, non.overlapping=FALSE, per.chromosome=FALSE, ...)

createRandomRegions(nregions=100, length.mean=250, length.sd=20, genome="hg19", mask=NULL, non.overlapping=FALSE)

resampleRegions(A, univers, per.chromosome=FALSE, ...)

Aaaaaalmost finished: Anyone with experience in packaging for Bioconductor?

Suggestions? Requests? Improvements?

Beta Testers Wanted

regioner an r/bioconductor package for the magement and comparision of genomic regions anna díez...

Documents