Revision d0c13affeb1def1f728f0e57c64e55fc9dc7cb25 authored by Alexey Sergushichev on 21 December 2019, 15:46:32 UTC, committed by Alexey Sergushichev on 21 December 2019, 15:46:32 UTC
1 parent d227226
calculatedAnnotation.R
#' Create calculated annotation
#'
#' \code{calculatedAnnotation} adds a column calculated by operation
#'
#' @param es ExpressionSet object.
#'
#' @param operation Name of the operation to perform calculation
#'
#' @param columns List of specified columns' indices (optional),
#' indices start from 0#'
#'
#' @param rows List of specified rows' indices (optional), indices start from 0
#'
#' @param name Name of the new annotation
#'
#' @param isColumns Apply fn to columns
#'
#' @return Nothing. Annotated dataset will be assigned to es in environment
#'
#' @import Biobase
#'
calculatedAnnotation <- function (es, operation, rows = c(),
columns = c(), isColumns = FALSE, name = NULL) {
rows <- getIndicesVector(rows, nrow(exprs(es)))
columns <- getIndicesVector(columns, ncol(exprs(es)))
fn <- tolower(operation)
if (!isColumns) {
fData(es)[[name]] <- NA
fData(es)[[name]][rows] <- apply(exprs(es[rows,columns]), 1, fn)
} else {
phenoData(es)[[name]] <- NA
phenoData(es)[[name]][columns] <- apply(exprs(es[rows,columns]), 2, fn)
}
assign("es", es, envir = parent.frame())
}

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