R/nFragments.R

In wrMisc: Analyze Experimental High-Throughput (Omics) Data

#' Number Of Fragments After Cut At Specific Character(s)
#'
#' This function tells the number of fragments/entry when cutting after 'cutAt' 
#' @param protSeq (character) text to be cut
#' @param cutAt (integer) position to cut
#' @param silent (logical) suppress messages if \code{TRUE}
#' @param debug (logical) additional messages for debugging
#' @param callFrom (character) allows easier tracking of messages produced
#' @return This function returns a numeric vector with number of fragments for each entry 'protSeq' (names are 'protSeq')
#' @seealso  more elaborate \code{{nFragments}}; \code{\link{cutAtMultSites}}
#' @examples
#' tmp <- "MSVSRTMEDSCELDLVYVTERIIAVSFPSTANEENFRSNLREVAQMLKSKHGGNYLLFNLSERRPDITKLHAKVLEFGWPDLHTPALEKI" 
#' nFragments0(c(tmp,"ojioRij"),c("R","K"))
#' @export
nFragments0 <- function(protSeq, cutAt, silent=FALSE, debug=FALSE, callFrom=NULL) {
  fxNa <- .composeCallName(callFrom, newNa="nFragments0")  
  sapply(protSeq, function(x) length(cutAtMultSites(x, cutAt)))}

#' Number Of Fragments After Cut At Specific Character(s) Within Size-range
#'
#' This function determines number of fragments /entry within range of 'sizeRa' (numeric,length=2) when cutting after 'cutAt' 
#' @param protSeq (character)  text to be cut
#' @param cutAt (character) position to cut
#' @param sizeRa (numeric,length=2) min and max size to consider
#' @param silent (logical) suppress messages if \code{TRUE}
#' @param debug (logical) additional messages for debugging
#' @param callFrom (character) allows easier tracking of messages produced
#' @return This function returns a numeric vector with number of fragments for each entry 'protSeq' (names are 'protSeq')
#' @seealso \code{\link{cutAtMultSites}}, simple version \code{{nFragments0}} (no size-range) 
#' @examples
#' tmp <- "MSVSREDSCELDLVYVTERIIAVSFPSTANEENFRSNLREVAQMLKSKHGGNYLLFNLSERRPDITKLHAKVLEFGWPDLHTPALEKI"
#' nFragments(c(tmp,"ojioRij"),c("R","K"),c(4,31))
#' 
#' @export
nFragments <- function(protSeq, cutAt, sizeRa, silent=FALSE, debug=FALSE, callFrom=NULL) {   # number of fragments /entry within range of 'sizeRa' (numeric,length=2) when cutting after 'cutAt' 
  fxNa <- .composeCallName(callFrom, newNa="nFragments")
  if(length(naOmit(unique(sizeRa))) <2) stop(" 'sizeRa' should be numeric of length=2")
  if(length(cutAt) <0) rep(1, length(protSeq)) else {
    sapply(protSeq, function(x) {y <- cutAtMultSites(x, cutAt)
    sum(nchar(y) > min(sizeRa, na.rm=TRUE) & nchar(y) < max(sizeRa,na.rm=TRUE), na.rm=TRUE)})}}