summarizeLdPerChr: Pairwise linkage disequilibrium

In timflutre/rutilstimflutre: Timothee Flutre's personal R code

Pairwise linkage disequilibrium

Description

Summarize estimates of linkage disequilibrium between pairs of SNPs belonging to the same chromosome over non-overlapping bins per chromosome.

Usage

summarizeLdPerChr(
  ld,
  coln.var = "cor2",
  coln.dist = "dist.locs",
  coln.chr = "chr",
  bin.width = 500,
  max.phy.len = 10^6,
  span = 0.75,
  nb.cores = 1,
  verbose = 0
)

Arguments

ld	data frame returned by estimLd
coln.var	name of the column in ld which contains the LD estimates
coln.dist	name of the column in ld which contains the physical distance between SNPs belonging to the same pair
coln.chr	name of the column in ld which contains the chromosome of each SNP pair
bin.width	width of each successive bin (they won't overlap)
max.phy.len	maximum physical length to consider
span	the parameter alpha which controls the degree of loess smoothing
nb.cores	the number of cores to use, i.e. at most how many child processes will be run simultaneously (not on Windows)
verbose	verbosity level (0/1)

Value

list with a list per chromosome with the LD summarized over bins as well as loess fits of LD vs mid bin

Author(s)

Timothee Flutre

See Also

summarizeLd

timflutre/rutilstimflutre documentation built on Feb. 7, 2024, 8:17 a.m.