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#####################################################################
#
# arithscan.R
#
# copyright (c) 2005-2019, Karl W Broman
# last modified Dec, 2019
# first written Mar, 2005
#
# This program is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License,
# version 3, as published by the Free Software Foundation.
#
# This program 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, version 3, for more details.
#
# A copy of the GNU General Public License, version 3, is available
# at http://www.r-project.org/Licenses/GPL-3
#
# Part of the R/qtl package
# Contains: +.scanone, -.scanone, +.scanoneperm, -.scanoneperm
# +.scantwo, -.scantwo, +.scantwoperm, -.scantwoperm
#
######################################################################
"-.scanone" <-
function(e1,e2)
{
if(!inherits(e1, "scanone"))
stop("Input should have class \"scanone\".")
if(missing(e2)) {
class(e1) <- "data.frame"
e1[,-(1:2)] <- -e1[,-(1:2)]
class(e1) <- c("scanone","data.frame")
return(e1)
}
if(!inherits(e2, "scanone"))
stop("Input should have class \"scanone\".")
class(e1) <- class(e2) <- "data.frame"
if(nrow(e1) != nrow(e2)) {
u1 <- levels(e1[,1])
u2 <- levels(e2[,2])
u <- unique(c(u1,u2))
if(length(u) == 0) stop("Can't subtract; no chromosomes in common.")
e1 <- e1[!is.na(match(e1[,1],u)),]
e2 <- e2[!is.na(match(e2[,1],u)),]
if(nrow(e1) != nrow(e2) || any(e1[,1] != e2[,1]) || max(abs(e1[,2]-e2[,2])) < 0.01)
stop("Can't subtract; arguments not compatible")
}
nc1 <- ncol(e1)
nc2 <- ncol(e2)
nc <- min(c(nc1,nc2))
e1 <- e1[,1:nc]
e1[,3:nc] <- e1[,3:nc] - e2[,3:nc]
# zero out small stuff
temp <- e1[,3:nc]
temp[!is.na(temp) & abs(temp) < 1e-6] <- 0
e1[,3:nc] <- temp
class(e1) <- c("scanone","data.frame")
e1
}
"+.scanone" <-
function(e1,e2)
{
if(!inherits(e1, "scanone"))
stop("Input should have class \"scanone\".")
if(missing(e2)) return(e1)
if(!inherits(e2, "scanone"))
stop("Input should have class \"scanone\".")
class(e1) <- class(e2) <- "data.frame"
if(nrow(e1) != nrow(e2)) {
u1 <- levels(e1[,1])
u2 <- levels(e2[,2])
u <- unique(c(u1,u2))
if(length(u) == 0) stop("Can't add; no chromosomes in common.")
e1 <- e1[!is.na(match(e1[,1],u)),]
e2 <- e2[!is.na(match(e2[,1],u)),]
if(nrow(e1) != nrow(e2) || any(e1[,1] != e2[,1]) || max(abs(e1[,2]-e2[,2])) < 0.01)
stop("Can't add; arguments not compatible")
}
nc1 <- ncol(e1)
nc2 <- ncol(e2)
nc <- min(c(nc1,nc2))
e1 <- e1[,1:nc]
e1[,3:nc] <- e1[,3:nc] + e2[,3:nc]
class(e1) <- c("scanone","data.frame")
e1
}
"-.scanoneperm" <-
function(e1, e2)
{
if(!inherits(e1, "scanoneperm"))
stop("Input should have class \"scanoneperm\".")
if(missing(e2)) {
e1.x <- ("xchr" %in% names(attributes(e1)))
if(e1.x) {
e1$A <- -e1$A
e1$X <- -e1$X
}
else {
theclass <- class(e1)
e1 <- -unclass(e1)
class(e1) <- theclass
}
return(e1)
}
if(!inherits(e2, "scanoneperm"))
stop("Input should have class \"scanoneperm\".")
# check input
e1.x <- ("xchr" %in% names(attributes(e1)))
e2.x <- ("xchr" %in% names(attributes(e2)))
if(e1.x != e2.x)
stop("Need both or neither input to be X-chr specific.\n")
if((e1.x && (any(dim(e1$A)!=dim(e2$A)) || any(dim(e1$X)!=dim(e2$X)))) ||
(!e1.x && any(dim(e1) != dim(e2))))
stop("Need input to concern the same phenotypes and no. permutations.\n")
if(e1.x) {
e1$A <- e1$A - e2$A
e1$X <- e1$X - e2$X
# zero out small stuff
e1$A[!is.na(e1$A) & abs(e1$A) < 1e-6] <- 0
e1$X[!is.na(e1$X) & abs(e1$X) < 1e-6] <- 0
}
else {
theclass <- class(e1)
e1 <- unclass(e1) - unclass(e2)
# zero out small stuff
e1[!is.na(e1) & abs(e1) < 1e-6] <- 0
class(e1) <- theclass
}
e1
}
"+.scanoneperm" <-
function(e1, e2)
{
if(!inherits(e1, "scanoneperm"))
stop("Input should have class \"scanoneperm\".")
if(missing(e2)) return(e1)
if(!inherits(e2, "scanoneperm"))
stop("Input should have class \"scanoneperm\".")
# check input
e1.x <- ("xchr" %in% names(attributes(e1)))
e2.x <- ("xchr" %in% names(attributes(e2)))
if(e1.x != e2.x)
stop("Need both or neither input to be X-chr specific.\n")
if((e1.x && (any(dim(e1$A)!=dim(e2$A)) || any(dim(e1$X)!=dim(e2$X)))) ||
(!e1.x && any(dim(e1) != dim(e2))))
stop("Need input to concern the same phenotypes and no. permutations.\n")
if(e1.x) {
e1$A <- e1$A + e2$A
e1$X <- e1$X + e2$X
}
else {
theclass <- class(e1)
e1 <- unclass(e1) + unclass(e2)
class(e1) <- theclass
}
e1
}
######################################################################
# -.scantwo: subtract LOD scores in two scantwo results
######################################################################
"-.scantwo" <-
function(e1, e2)
{
if(!inherits(e1, "scantwo"))
stop("Input should have class \"scantwo\".")
if(missing(e2)) {
e1$lod <- -e1$lod
if("scanoneX" %in% names(e1))
e1$scanoneX <- -e1$scanoneX
return(e1)
}
if(!inherits(e2, "scantwo"))
stop("Input should have class \"scantwo\".")
e1x <- "scanoneX" %in% names(e1)
e2x <- "scanoneX" %in% names(e2)
if(any(dim(e1$map) != dim(e2$map)) ||
length(dim(e1$lod)) != length(dim(e2$lod)) ||
any(dim(e1$lod) != dim(e2$lod)) || e1x != e2x)
stop("input arguments do not conform.")
e1$lod <- e1$lod - e2$lod
if(e1x) {
if(!is.null(e1$scanoneX) && !is.null(e2$scanoneX))
e1$scanoneX <- e1$scanoneX - e2$scanoneX
}
e1
}
######################################################################
# +.scantwo: add LOD scores in two scantwo results
######################################################################
"+.scantwo" <-
function(e1, e2)
{
if(!inherits(e1, "scantwo"))
stop("Input should have class \"scantwo\".")
if(missing(e2)) return(e1)
if(!inherits(e2, "scantwo"))
stop("Input should have class \"scantwo\".")
e1x <- "scanoneX" %in% names(e1)
e2x <- "scanoneX" %in% names(e2)
if(any(dim(e1$map) != dim(e2$map)) ||
length(dim(e1$lod)) != length(dim(e2$lod)) ||
any(dim(e1$lod) != dim(e2$lod)) || e1x != e2x)
stop("input arguments do not conform.")
e1$lod <- e1$lod + e2$lod
if(e1x) {
if(!is.null(e1$scanoneX) && !is.null(e2$scanoneX))
e1$scanoneX <- e1$scanoneX + e2$scanoneX
}
e1
}
######################################################################
# -.scantwoperm: subtract LOD scores in two scantwo permutation results
######################################################################
"-.scantwoperm" <-
function(e1, e2)
{
if(!inherits(e1, "scantwoperm"))
stop("Input should have class \"scantwoperm\".")
if(missing(e2)) {
# x-chr-specific
if("AA" %in% names(e1)) {
for(i in seq(along=e1))
for(j in seq(along=e1[[i]]))
e1[[i]][[j]] <- -e1[[i]][[j]]
return(e1)
}
for(i in 1:length(e1))
e1[[i]] <- -e1[[i]]
return(e1)
}
if(!inherits(e2, "scantwoperm"))
stop("Input should have class \"scantwoperm\".")
# x-chr-specific
if("AA" %in% names(e1) || "AA" %in% names(e2)) {
if(!("AA" %in% names(e1) && "AA" %in% names(e2)))
stop("Input must both be Xchr-specific, or neither")
for(i in seq(along=e1)) {
for(j in seq(along=e1[[i]])) {
if(any(dim(e1[[i]][[j]]) != dim(e1[[i]][[j]])))
stop("dimensions do not match")
e1[[i]][[j]] <- e1[[i]][[j]] - e2[[i]][[j]]
}
}
return(e1)
}
dim1 <- sapply(e1, dim)
dim2 <- sapply(e2, dim)
if(any(dim1 != dim2))
stop("Need input to concern the same phenotypes and no. permutations.\n")
for(i in 1:length(e1))
e1[[i]] <- e1[[i]] - e2[[i]]
e1
}
######################################################################
# +.scantwoperm: add LOD scores in two scantwo permutation results
######################################################################
"+.scantwoperm" <-
function(e1, e2)
{
if(!inherits(e1, "scantwoperm"))
stop("Input should have class \"scantwoperm\".")
if(missing(e2)) return(e1)
if(!inherits(e2, "scantwoperm"))
stop("Input should have class \"scantwoperm\".")
# x-chr-specific
if("AA" %in% names(e1) || "AA" %in% names(e2)) {
if(!("AA" %in% names(e1) && "AA" %in% names(e2)))
stop("Input must both be Xchr-specific, or neither")
for(i in seq(along=e1)) {
for(j in seq(along=e1[[i]])) {
if(any(dim(e1[[i]][[j]]) != dim(e1[[i]][[j]])))
stop("dimensions do not match")
e1[[i]][[j]] <- e1[[i]][[j]] + e2[[i]][[j]]
}
}
return(e1)
}
dim1 <- sapply(e1, dim)
dim2 <- sapply(e2, dim)
if(any(dim1 != dim2))
stop("Need input to concern the same phenotypes and no. permutations.\n")
for(i in 1:length(e1))
e1[[i]] <- e1[[i]] + e2[[i]]
e1
}
# end of arithscan.R
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