R/combine_data_spg_function.R

In tydarnell/GeneticMediation: An R Package for Causal Mediation Analysis of ROSMAP Data

#' Combine Data SNP-Peak-Gene
#'
#' @description SNP-Peak-Gene Data: combine projid, SNPs, PCs, membership,
#'   age, gender, peaks, gene and outcome data for a chromosome.
#' @param chr chromosome name
#' @keywords dataprep spg
#' @export

combine_data_spg <- function(chr) {
    load(paste("data/mediator/mediation_", chr, "_new.RData", sep = ""))
    load(paste("data/peak.data/peak.data_", chr, ".RData", sep = ""))
    SNP.cov.data = merge(SNP.pc.data, phenotype.data[, c("projid", "plaq_n_sqr")], by = "projid", 
        all = F)
    disease.data = phenotype.data[, c("projid", "plaq_n_sqr")]
    genes = unique(subset(genebysnp, Chr == chr)$gene)
    n.gene = length(colnames(gene.data))
    gene.name = colnames(gene.data)[-c(n.gene - 1, n.gene)]
    colnames(gene.data)[-c(n.gene - 1, n.gene)] = paste("g", gene.name, sep = "")
    gene.med = gene.data[, c("projid", "Phase", genes)]
    med.data = Reduce(function(x, y) merge(x, y, all = F, by = "projid"), list(SNP.cov.data, peak.data, 
        gene.med, disease.data))
    med.data = unique(med.data)
    med.data$membership = factor(med.data$membership)
    med.data$Phase <- factor(med.data$Phase)
    med.data
}