getLogitFracMeth {biscuiteer} | R Documentation |
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.
getLogitFracMeth(x, minCov = 3, minSamp = 2, k = 0.1, r = NULL) getMvals(x, minCov = 3, minSamp = 2, k = 0.1, r = NULL)
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) |
Smoothed logit(M / Cov) GRanges with coordinates as row names
getMvals
: Alias for getLogitFracMeth
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)