Nothing
# Copyright 2006 Laboratoire de Biologie et de Biometrie Appliquée
# (UMR 5558);CNRS; Univ. Lyon 1, 43 bd 11 nov, 69622,
# Villeurbanne Cedex, France.
#
# This file is part of MMSlidingWindow.
#
# MMSlidingWindow is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License, or
# (at your option) any later version.
#
# MMSlidingWindow is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with MMSlidingWindow; if not, write to the Free Software
# Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
#--- class definition
setClass("MMSlidingWindow",
contains = "Interpolation",
representation(
name = "character",
size = "integer",
shift = "integer",
threshold = "integer",
results = "vector",
geneticalDistances = "vector"
),
prototype(
name = "slidingwindow",
size = as.integer(1000000),
shift = as.integer(500000),
threshold = as.integer(8),
results = vector(),
geneticalDistances = vector()
)
)
#--- constructors
setGeneric("MMSlidingWindow", function(val) standardGeneric("MMSlidingWindow"))
setMethod("MMSlidingWindow", signature(val = "missing"), function(val) {
object <- new("MMSlidingWindow")
object@visible <- T
object@color <- "#000000"
object
})
#--- accessors
setMethod("name", "Interpolation", function(object) object@name)
setGeneric("size", function(object) standardGeneric("size"))
setMethod("size", "MMSlidingWindow", function(object) object@size)
setGeneric("shift", function(object) standardGeneric("shift"))
setMethod("shift", "MMSlidingWindow", function(object) object@shift)
setGeneric("threshold", function(object) standardGeneric("threshold"))
setMethod("threshold", "MMSlidingWindow", function(object) object@threshold)
#--- replacement methods
setReplaceMethod("name", "Interpolation", function(object, value) {
object@name<-value
object
})
setGeneric("size<-", function(object, value) standardGeneric("size<-"))
setReplaceMethod("size", "MMSlidingWindow", function(object, value) {
if(value > 0)
object@size <- as.integer(value)
object
})
setGeneric("shift<-", function(object, value) standardGeneric("shift<-"))
setReplaceMethod("shift","MMSlidingWindow", function(object, value) {
if(value > 0)
object@shift <- as.integer(value)
object
})
setGeneric("threshold<-", function(object, value) standardGeneric("threshold<-"))
setReplaceMethod("threshold", "MMSlidingWindow", function(object, value) {
if(value > 0)
object@threshold <- as.integer(value)
object
})
#--- query
setMethod("query", c("MMSlidingWindow", "numeric"), function(object, pos) {
sapply(pos, function(pp) {
if(pp < min(object@physicalPositions, na.rm = TRUE) || pp > max(object@physicalPositions, na.rm = TRUE))
return(NA)
btm <- pp - object@size / 2
top <- pp + object@size / 2
idx <- which((object@physicalPositions >= btm) & (object@physicalPositions <= top))
if(length(idx) < object@threshold)
return(NA)
mkrphys <- object@physicalPositions[idx]
mkrgen <- object@geneticalDistances[idx]
lm1 <- lm(mkrgen ~ mkrphys)
round(lm1$coef[[2]] * 1000000, digits = 2)
})
})
#--- queryModel -- non exported
setGeneric("queryModel", function(object, pos) standardGeneric("queryModel"))
setMethod("queryModel", c("MMSlidingWindow","numeric"), function(object, pos) {
sapply(pos, function(pp) {
if(pp < min(object@physicalPositions, na.rm = TRUE) || pp > max(object@physicalPositions, na.rm = TRUE))
return(NA)
btm <- pp - object@size / 2
top <- pp + object@size / 2
idx <- which((object@physicalPositions >= btm) & (object@physicalPositions <= top))
if(length(idx) < object@threshold)
return(NA)
mkrphys <- object@physicalPositions[idx]
mkrgen <- object@geneticalDistances[idx]
lm1 <- lm(mkrgen ~ mkrphys)
lm1$coef[[1]] + lm1$coef[[2]] * pp
})
})
#--- interpolate
setMethod("interpolate", signature(object = "MMSlidingWindow", map = "MareyMap"), function(object, map) {
end <- max(physicalPositions(map))
valgen <- geneticDistances(map)[which(markerValidity(map))]
valphys <- physicalPositions(map)[which(markerValidity(map))]
object@physicalPositions <- valphys
object@geneticalDistances <- valgen
object@rates <- query(object, physicalPositions(map))
object
})
#--- plot
setMethod("plot", c("MareyMap", "MMSlidingWindow"), function(x, y, ...) {
plotModel(y, ...)
par(new = T)
plotRates(y, ...)
})
#--- plotModel
setMethod("plotModel", "MMSlidingWindow", function(object, ...) {
cl <- match.call()
cl[[1]] <- as.name("plot")
cl$object <- NULL
cl$col <- object@color
cl$type <- "l"
expli <- seq(object@size / 2, max(object@physicalPositions), object@shift)
cl$x <- expli / 1000000
cl$y <- queryModel(object, expli)
eval(cl)
})
#--- plotRate
setMethod("plotRate", "MMSlidingWindow", function(object, ...) {
cl <- match.call()
cl[[1]] <- as.name("plot")
cl$object <- NULL
cl$col <- object@color
cl$type <- "l"
expli <- seq(object@size / 2, max(object@physicalPositions), object@shift)
cl$x <- expli / 1000000
cl$y <- query(object, expli)
eval(cl)
})
#--- createOrder
setMethod("createOrder", "MMSlidingWindow", function(object) {
paste("new(\"MMSlidingWindow\", name = \"", object@name, "\", ", argList(object), ", size = as.integer(", object@size, "), shift = as.integer(", object@shift, "), threshold = as.integer(", object@threshold, "))", sep = "")
})
#--- userParam
setMethod("userParam", "MMSlidingWindow", function(object) {
nam <- InterpolationParam()
paramName(nam) <- "Name"
paramDesc(nam) <- " The name of the interpolation "
paramType(nam) <- "character"
paramDefault(nam) <- "slidingwindow"
paramMin(nam) <- 1
paramMax(nam) <- NULL
paramFun(nam) <- "name"
size <- InterpolationParam()
paramName(size) <- "Size"
paramDesc(size) <- " Size of the sliding window in base pair "
paramType(size) <- "integer"
paramDefault(size) <- 3000000
paramMin(size) <- 2
paramFun(size) <- "size"
shift <- InterpolationParam()
paramName(shift) <- "Shift"
paramDesc(shift) <- " Shift between two consecutive windows in base pair "
paramType(shift) <- "integer"
paramDefault(shift) <- 500000
paramMin(shift) <- 1
paramFun(shift) <- "shift"
thr <- InterpolationParam()
paramName(thr) <- "Threshold"
paramDesc(thr) <- " Minimum number of markers by window "
paramType(thr) <- "integer"
paramDefault(thr) <- 5
paramMin(thr) <- 2
paramFun(thr) <- "threshold"
c(list(nam), userParam(as(object, "Interpolation")), list(size, shift, thr))
})
registerInterpolationMethod("Fixed size sliding window method", "MMSlidingWindow")
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.