R/norm_by_ref.R

In vladpetyuk/vp.misc: Miscellaneous functions used by Vlad Petyuk for proteomics data analysis

#' Normalization of SRM Data
#' 
#' Subtracts expression data of one condition from another. 
#' Converts one MSnSet to another MSnSet.
#' 
#' @param m MSnSet object
#' @param exprsn expression with proteins as terms.  
#'          It is evaluated and used as reference.
#'          
#' @importFrom Biobase exprs
#' @export normalizeByRef

normalizeByRef <- function(m, exprsn){
    #
    ref.call <- substitute(exprsn)
    ref <- eval(ref.call, envir = data.frame(t(exprs(m))))
    exprs(m) <- sweep(exprs(m), 2, ref, '-') # must be log scale 
    return(m)
    
}

# normalizeByRef(m, MBP.1)
# normalizeByRef(m, TH.2)
# normalizeByRef(m, (MBP.1+TH.2)/2)