imputeBetasByGenomicNeighbors: Impute missing data based on genomic neighbors.

In zwdzwd/sesame: SEnsible Step-wise Analysis of DNA MEthylation BeadChips

Impute missing data based on genomic neighbors.

Description

Impute missing data based on genomic neighbors.

Usage

imputeBetasByGenomicNeighbors(
  betas,
  platform = NULL,
  BPPARAM = SerialParam(),
  max_neighbors = 3,
  max_dist = 10000
)

Arguments

betas	named vector of beta values
platform	platform
BPPARAM	use MulticoreParam(n) for parallel processing
max_neighbors	maximum neighbors to use for dense regions
max_dist	maximum distance to count as neighbor

Value

imputed data, vector or matrix

Examples

betas = openSesame(sesameDataGet("EPICv2.8.SigDF")[[1]])
sum(is.na(betas))
betas2 = imputeBetasByGenomicNeighbors(betas, "EPICv2")
sum(is.na(betas2))

zwdzwd/sesame documentation built on Dec. 21, 2024, 1:20 p.m.