match_maker: Weighted matching of controls to cases using PCA results.

In PCAmatchR: Match Cases to Controls Based on Genotype Principal Components

Weighted matching of controls to cases using PCA results.

Description

Weighted matching of controls to cases using PCA results.

Usage

match_maker(
  PC = NULL,
  eigen_value = NULL,
  data = NULL,
  ids = NULL,
  case_control = NULL,
  num_controls = 1,
  num_PCs = NULL,
  eigen_sum = NULL,
  exact_match = NULL,
  weight_dist = TRUE,
  weights = NULL
)

Arguments

PC	Individual level principal component.
eigen_value	Computed eigenvalue for each PC. Used as the numerator to calculate the percent variance explained by each PC.
data	Dataframe containing id and case/control status. Optionally includes covariate data for exact matching.
ids	The unique id variable contained in both "PC" and "data."
case_control	The case control status variable.
num_controls	The number of controls to match to each case. Default is 1:1 matching.
num_PCs	The total number of PCs calculated within the PCA. Can be used as the denomiator to calculate the percent variance explained by each PC. Default is 1000.
eigen_sum	The sum of all possible eigenvalues within the PCA. Can be used as the denomiator to calculate the percent variance explained by each PC.
exact_match	Optional variables contained in the dataframe on which to perform exact matching (i.e. sex, race, etc.).
weight_dist	When set to true, matches are produced based on PC weighted Mahalanobis distance. Default is TRUE.
weights	Optional user defined weights used to compute the weighted Mahalanobis distance metric.

Value

A list of matches and weights.

Examples

# Create PC data frame by subsetting provided example dataset
pcs <- as.data.frame(PCs_1000G[,c(1,5:24)])
# Create eigenvalues vector using example dataset
eigen_vals <- c(eigenvalues_1000G)$eigen_values
# Create full eigenvalues vector using example dataset
all_eigen_vals<- c(eigenvalues_all_1000G)$eigen_values
# Create Covarite data frame
cov_data <- PCs_1000G[,c(1:4)]
# Generate a case status variable using ESN 1000 Genome population
cov_data$case <- ifelse(cov_data$pop=="ESN", c(1), c(0))
# With 1 to 1 matching
if(requireNamespace("optmatch", quietly = TRUE)){
                        library(optmatch)
                        match_maker(PC = pcs,
                                    eigen_value = eigen_vals,
                                    data = cov_data,
                                    ids = c("sample"),
                                    case_control = c("case"),
                                    num_controls = 1,
                                    eigen_sum = sum(all_eigen_vals),
                                    weight_dist=TRUE
                                   )
                        }

PCAmatchR documentation built on Dec. 1, 2022, 1:33 a.m.