R/createDesignMatrix.R

In UW-GAC/GENESIS: GENetic EStimation and Inference in Structured samples (GENESIS): Statistical methods for analyzing genetic data from samples with population structure and/or relatedness

createDesignMatrix <- function(x, outcome, covars=NULL, group.var=NULL) {

    # remake factors to remove any missing levels
    for (f in union(covars, group.var)) {
        if(is.factor(x[[f]]) & !is.ordered(x[[f]])) {
            x[[f]] <- factor(x[[f]])
        }
    }

    if (!is.null(covars)) {
        model.formula <- as.formula(paste(outcome, "~", paste(covars, collapse="+")))
        # allow interactions
        covars <- unique(unlist(strsplit(covars,"[*:]")))
    } else {
        model.formula <- as.formula(paste(outcome, "~", 1))
    }
    x <- x[, unique(c(outcome, covars, group.var)), drop=FALSE]
    x <- x[complete.cases(x),,drop=FALSE]

    # group index
    if (!is.null(group.var)) {
        group.idx <- .indexList(x[[group.var]])
    } else {
        group.idx <- NULL
    }

    # outcome vector - preserve column name
    #y <- x[[outcome]]
    y <- as.matrix(x[,outcome,drop=FALSE])
    # create design matrix
    X <- model.matrix(model.formula, data=x)
    # check for columns of all the same value (except the intercept)
    dropcol <- append(FALSE, apply(X[,-1,drop=FALSE], 2, var) == 0)
    if (sum(dropcol) > 0) {
        message("Covariates ",paste(colnames(X)[dropcol], collapse = ", "), " have only 1 value: they have been removed from the model")
        X <- X[,!dropcol,drop=FALSE]
    }

    # Check that design matrix is not collinear.
    rank <- Matrix::rankMatrix(X)
    if (rank < ncol(X)) {
      err <- "Design matrix is not full rank; the model can not be fit. Check for multicollinearity among your covariates."
      stop(err)
    }
    list(y=y, X=X, group.idx=group.idx)
}

.indexList <- function(x) {
    groups <- unique(x)
    idx <- lapply(groups, function(g) which(x == g))
    names(idx) <- as.character(groups)
    idx
}