bootRanges {nullranges}R Documentation

Block bootstrap for genomic ranges

Description

Performs a block bootstrap, optionally with respect to a genome segmentation. Returns a bootRanges object, which is a GRanges object with all the ranges concatenated, and iteration and block length indicated by metadata columns

Usage

bootRanges(
  y,
  blockLength,
  R = 1,
  seg = NULL,
  exclude = NULL,
  excludeOption = c("drop", "trim"),
  proportionLength = TRUE,
  type = c("bootstrap", "permute"),
  withinChrom = FALSE
)

Arguments

y

the GRanges to bootstrap sample

blockLength

the length of the blocks (for proportional blocks, this is the maximal length of a block)

R

the number of bootstrap samples to generate

seg

the segmentation GRanges, with a column ("state") indicating segmentation state (optional)

exclude

the GRanges of excluded regions (optional)

excludeOption

whether to "drop" or "trim" bootstrap ranges that overlap a excluded region

proportionLength

for the segmented block bootstrap, whether to use scaled block lengths, (scaling by the proportion of the segmentation state out of the total genome length)

type

the type of null generation (un-segmented bootstrap only)

withinChrom

whether to re-sample (bootstrap) ranges across chromosomes (default) or only within chromosomes (un-segmented bootstrap only)

Value

a bootRanges (GRanges object) with the bootstrapped ranges, where iteration and block length are recorded as metadata columns

Examples


set.seed(1)
library(GenomicRanges)
gr <- GRanges("chr1", IRanges(0:4 * 10 + 1, width=5),
              seqlengths=c(chr1=50))
br <- bootRanges(gr, blockLength=10)


[Package nullranges version 1.0.1 Index]