byExtremality: Choose loci or features by extremality

In trichelab/biscuitEater: Convenience Functions for Biscuit

Choose loci or features by extremality

Description

This function finds the k most extremal features (features above a certain fraction of the Bernoulli variance) in 'bsseq' and returns their values.

Usage

byExtremality(bsseq, r = NULL, k = 500)

Arguments

bsseq	A bsseq object
r	Regions to consider - NULL covers all loci (DEFAULT: NULL)
k	How many rows/regions to return (DEFAULT: 500)

Details

For DNA methylation, particularly when summarized across regions, we can do better (a lot better) than MAD. Since we know: max(SD(X_j)) if X_j ~ Beta(a, b) < max(SD(X_j)) if X_j ~ Bernoulli(a/(a+b)) for X with a known mean and standard deviation (SD), then we can solve for (a+b) by MoM. We can then define the extremality by: extremality = sd(X_j) / bernoulliSD(mean(X_j))

Value

  A GRanges object with methylation values sorted by extremality

Examples

  shuf_bed <- system.file("extdata", "MCF7_Cunha_chr11p15_shuffled.bed.gz",
                          package="biscuiteer")
  orig_bed <- system.file("extdata", "MCF7_Cunha_chr11p15.bed.gz",
                          package="biscuiteer")
  shuf_vcf <- system.file("extdata",
                          "MCF7_Cunha_shuffled_header_only.vcf.gz",
                          package="biscuiteer")
  orig_vcf <- system.file("extdata",
                          "MCF7_Cunha_header_only.vcf.gz",
                          package="biscuiteer")
  bisc1 <- readBiscuit(BEDfile = shuf_bed, VCFfile = shuf_vcf,
                       merged = FALSE)
  bisc2 <- readBiscuit(BEDfile = orig_bed, VCFfile = orig_vcf,
                       merged = FALSE)

  reg <- GRanges(seqnames = rep("chr11",5),
                 strand = rep("*",5),
                 ranges = IRanges(start = c(0,2.8e6,1.17e7,1.38e7,1.69e7),
                                  end= c(2.8e6,1.17e7,1.38e7,1.69e7,2.2e7))
                 )

  comb <- unionize(bisc1, bisc2)

  ext <- byExtremality(comb, r = reg)

trichelab/biscuitEater documentation built on March 2, 2024, 6:57 p.m.