R/CBS.SMOOTH.R

In PSCBS: Analysis of Parent-Specific DNA Copy Numbers

###########################################################################/**
# @set class=CBS
# @RdocMethod getSmoothLocusData
#
# @title "Gets smoothed locus-level data"
#
# \description{
#  @get "title".
# }
#
# @synopsis
#
# \arguments{
#   \item{fit}{An @see "CBS" object.}
#   \item{by}{A @numeric scalar specifying the bin size.}
#   \item{...}{Not used.}
# }
#
# \value{
#   Returns a @data.frame where the
#   first three columns are 'chromosome', 'x' (position),
#   and 'count' (number of loci average over for the given bin),
#   and the remaining ones are the smoothed locus-level data.
# }
#
# @author "HB"
#
# \seealso{
#   @seeclass
# }
#
# @keyword internal
#*/###########################################################################
setMethodS3("getSmoothLocusData", "CBS", function(fit, by, ...) {
  # Argument 'by':
  by <- Arguments$getNumeric(by, range=c(0,Inf))

  chromosomes <- getChromosomes(fit)
  data <- getLocusData(fit)

  chromosome <- NULL; rm(list="chromosome") # To please R CMD check

  dataS <- NULL
  for (kk in seq_along(chromosomes)) {
    chr <- chromosomes[kk]
    dataT <- subset(data, chromosome == chr)
    x <- dataT$x
    y <- dataT$y
    rx <- range(x, na.rm=TRUE)
    bx <- seq(from=rx[1], to=rx[2], by=by)
    xS <- bx[-1] - by/2
    yS <- binMeans(y=y, x=x, bx=bx)
    count <- attr(yS, "count")
    yS[count == 0L] <- NA_real_
    attr(yS, "count") <- NULL
    dataTS <- data.frame(chromosome=chr, x=xS, count=count, y=yS)
    dataS <- rbind(dataS, dataTS)
  } # for (kk ...)

  dataS
}, protected=TRUE) # getSmoothLocusData()