TRACE: TRACE: fasT and Robust Ancestry Coordinate Estimation

In Yi-Jiang/MethyGenotyper: MethylGenotyper: Accurate estimation of SNP genotypes from DNA methylation data

TRACE: fasT and Robust Ancestry Coordinate Estimation

Description

Adapted from http://csg.sph.umich.edu/chaolong/LASER

Usage

TRACE(
  refGeno,
  studyGeno,
  MIN_LOCI = 100,
  DIM = 4,
  DIM_HIGH = 20,
  MAX_ITER = 10000,
  THRESHOLD = 1e-06,
  cpu = 1
)

Arguments

refGeno	A matrix of genotypes of reference individuals. Provide probes as rows and samples as columns.
studyGeno	A matrix of genotypes of study samples. Provide probes as rows and samples as columns.
MIN_LOCI	Minimum number of non-missing loci required
DIM	Number of PCs in the reference to match
DIM_HIGH	Number of PCs for sample-specific PCA
MAX_ITER	Maximum iterations for the projection Procrustes analysis
THRESHOLD	Convergence criterion for the projection Procrustes analysis
cpu	Number of CPU.

Value

A list containing

refPC	Top PCs in the reference
studyPC	Top PCs in study samples

Yi-Jiang/MethyGenotyper documentation built on Sept. 4, 2024, 12:47 p.m.