getLogitFracMeth: Helper function for compartment inference

In trichelab/biscuitEater: Convenience Functions for Biscuit

Helper function for compartment inference

Description

Want an object with nominally Gaussian error for compartment inference, so this function uses 'suitable' (defaults to to 3 or more reads in 2 or more samples) measurements. Using Dirichlet smoothing (adding 'k' reads to M and U), these measurements are then turned into lightly moderated, logit-transformed methylated-fraction estimates for compartment calling.

Usage

getLogitFracMeth(x, minCov = 3, minSamp = 2, k = 0.1, r = NULL)

getMvals(x, minCov = 3, minSamp = 2, k = 0.1, r = NULL)

Arguments

x	A bsseq object with methylated and total reads
minCov	Minimum read coverage for landmarking samples (DEFAULT: 3)
minSamp	Minimum landmark samples with at least minCov (DEFAULT: 2)
k	Pseudoreads for smoothing (DEFAULT: 0.1)
r	Regions to collapse over - if NULL, do it by CpG (DEFAULT: NULL)

Value

    Smoothed logit(M / Cov) GRanges with coordinates as row names

Functions

• getMvals(): Alias for getLogitFracMeth

Examples

  orig_bed <- system.file("extdata", "MCF7_Cunha_chr11p15.bed.gz",
                          package="biscuiteer")
  orig_vcf <- system.file("extdata", "MCF7_Cunha_header_only.vcf.gz",
                          package="biscuiteer")
  bisc <- 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))
                 )

  frac <- getLogitFracMeth(bisc, minSamp = 1, r = reg)

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