compare_cell_fraction_estimates: Compares cell fraction estimates from EpiDISH and TCA under...

In cozygene/CellTypeSpecificMethylationAnalysis: Evaluation of Cell Type Specific Methylation Analysis

Description

Compares cell fraction estimates from EpiDISH and TCA under several models

Usage

compare_cell_fraction_estimates(
  X,
  W.facs,
  C1 = NULL,
  C2 = NULL,
  random_seed = 1000,
  verbose = TRUE
)

Arguments

X	Matrix of methylation values with column names as samples and row names as sites
W.facs	Matrix of FACS derived cell type fractions with column names as cell types and row names as samples
C1	Matrix of source-specific covariates for TCA with column names as features and row names as samples
C2	Matrix of mixture-level covariates for TCA with column names as features and row names as samples
random_seed	Random seed for replication
verbose	Boolean for printing out progress

Value

A list of results. Slot performance.metrics contains a dataframe where each row indicates either the PCC or RMSE of a method for estimating a specific cell type fraction. Slot prop.estimates contains a list of fractions estimated by each method.

cozygene/CellTypeSpecificMethylationAnalysis documentation built on Jan. 28, 2022, 11:20 a.m.