R/reformate_for_matrixEQTL.R

In cfbeuchel/CarlHelpR: A Package With Functions

#' Reformate For MatrixEQTL.
#'
#' Function to transpose data for processing in MatrixEQTL.
#'
#' Author: Holger Kirsten
#'
#' @param metab4_m_po The data.table to reformat
#'
#' @param idvar The column name specifying the probe IDs
#'
#' @export

reformate_for_matrixEQTL <- function(metab4_m_po, idvar = "pid") {
    print(file_preview(metab4_m_po))
    move_col_front(metab4_m_po, idvar)
    metab4_m_po <- t(metab4_m_po)
    colnames(metab4_m_po) <- metab4_m_po[idvar, ]
    metab4_m_po <- metab4_m_po[-1, ]
    myrownames <- rownames(metab4_m_po)
    metab4_m_po <- apply(metab4_m_po, 2, function(x) as.numeric(x))
    metab4_m_po <- data.table::data.table(id = myrownames, metab4_m_po)
    print(file_preview(metab4_m_po))
    metab4_m_po
}