inst/unitTests/test_FAData.R
In EuracBiomedicalResearch/FamAgg: Pedigree Analysis and Familial Aggregation
.getMinSub <- function(){
data(minnbreast)
mbsub <- minnbreast[minnbreast$famid %in% 4:19, ]
return(mbsub)
}
mbsub <- .getMinSub()
test_show <- function() {
mbped <- mbsub[, c("famid", "id", "fatherid", "motherid", "sex")]
colnames(mbped) <- FamAgg:::.PEDCN
fad <- FAData(pedigree=mbped)
res <- capture.output(show(fad))
checkEquals(res[1], "FAData object with:")
}
test_construct <- function(){
mbped <- mbsub[, c("famid", "id", "fatherid", "motherid", "sex")]
colnames(mbped) <- FamAgg:::.PEDCN
fad <- FAData(pedigree=mbped)
tcancer <- mbsub$cancer
names(tcancer) <- mbsub$id
trait(fad) <- tcancer
## constructor with the trait
fad <- FAData(pedigree=mbped, trait=mbsub$cancer)
tcancershuffle <- sample(tcancer, length(tcancer))
trait(fad) <- tcancershuffle
## the function internally has to rematch the ids
checkEquals(trait(fad), tcancer)
## testing the $ accessor
checkEquals(fad$trait, tcancer)
fad@traitname <- "cancer"
checkEquals(fad$cancer, tcancer)
## check if the pedigree returns the correct extended pedigree
## with the additional column affected
ped <- pedigree(fad)
fromPed <- ped$affected
names(fromPed) <- ped$id
checkEquals(fromPed, tcancer)
## test affected and phenotyped individuals
affIds <- affectedIndividuals(fad)
checkEquals(affIds, as.character(ped$id[which(ped$affected == 1)]))
phenoIds <- phenotypedIndividuals(fad)
checkEquals(phenoIds, as.character(ped$id[!is.na(ped$affected)]))
## check if a logical trait is handled properly
tcancerrandom <- sample(c(rep(T, 3), rep(F, 7), NA), size=length(tcancer),
replace = TRUE)
names(tcancerrandom) <- names(tcancer)
fad1 <- FAData(pedigree=mbped, trait=tcancerrandom)
fad2 <- FAData(pedigree=mbped)
trait(fad2) <- tcancerrandom
checkEquals(trait(fad1), trait(fad2))
tcint <- as.integer(tcancerrandom)
names(tcint) <- names(tcancerrandom)
checkEquals(trait(fad1), tcint)
}
test_FAData_from_file <- function(){
## create from file
pedfile <- system.file("txt/minnbreastsub.txt", package="FamAgg")
checkException(fad2 <- FAData(pedfile, id.col="ID" ))
fad2 <- FAData(pedfile, id.col="id", family.col="famid", father.col="fatherid",
mother.col="motherid", sex.col="sex", header=TRUE)
## Now read it from ped
pedfile <- system.file("txt/minnbreastsub.ped.gz", package="FamAgg")
fadPed <- FAData(pedfile)
pedfile <- system.file("txt/minnbreastsub-bad.ped.gz", package="FamAgg")
checkException(FAData(pedfile))
}
## Testing the validation methods
test_validate <- function(){
tmpPed <- mbsub[, c("famid", "id", "fatherid", "motherid", "sex")]
colnames(tmpPed) <- FamAgg:::.PEDCN
## Don't allow NAs in id, father or mother
badPed <- tmpPed
badPed[13, "id"] <- NA
checkException(FAData(badPed))
badPed <- tmpPed
badPed[13, "father"] <- NA
checkException(FAData(badPed))
badPed <- tmpPed
badPed[13, "mother"] <- NA
checkException(FAData(badPed))
## Don't allow father or mother ids other than 0 or %in% $id
badPed <- tmpPed
badPed[13, "mother"] <- "123345"
checkException(FAData(badPed))
badPed <- tmpPed
badPed[13, "father"] <- "123345"
checkException(FAData(badPed))
}
## OK, 0.0.6
test_age <- function(){
mbped <- mbsub[, c("famid", "id", "fatherid", "motherid", "sex")]
colnames(mbped) <- FamAgg:::.PEDCN
tmp <- new("FAData")
ages <- mbsub$endage
names(ages) <- mbped$id
## Setting ages to a empty object should not add age.
age(tmp) <- ages
checkEquals(length(age(tmp)), 0)
checkTrue(validObject(tmp))
## With pedigree:
pedigree(tmp) <- mbped
checkTrue(validObject(tmp))
age(tmp) <- ages
checkEqualsNumeric(length(age(tmp)), length(ages))
checkEqualsNumeric(length(age(tmp)), nrow(mbped))
checkEquals(names(age(tmp)), as.character(mbped[, 2]))
}
test_pedigree <- function(){
tmp <- new("FAData")
## mbsub <- .getMinSub()
PedDf <- mbsub[, c("famid", "id", "fatherid", "motherid", "sex")]
colnames(PedDf) <- FamAgg:::.PEDCN
pedigree(tmp) <- PedDf
checkTrue(is(pedigree(tmp, return.type="data.frame"), "data.frame"))
tmp2 <- pedigree(tmp, return.type="data.frame")
## have to transform sex into a factor...
PedDf$sex <- factor(PedDf$sex, levels=c("M", "F"))
rownames(PedDf) <- as.character(PedDf$id)
checkEquals(tmp2, FamAgg:::sanitizePed(PedDf))
## submit a pedigree(List) object...
Ped <- pedigree(id=PedDf[, 2], famid=PedDf[, 1], dadid=PedDf[, 3],
momid=PedDf[, 4], sex=PedDf[, 5])
pedigree(tmp) <- Ped
checkTrue(is(pedigree(tmp, return.type="pedigree"), "pedigreeList"))
## check the Ped with the pedigree(tmp)
tmp1 <- do.call(cbind, Ped)
tmp2 <- do.call(cbind, pedigree(tmp, return.type="pedigree"))
checkEquals(tmp1, tmp2)
}
test_subset <- function(){
do.plot <- FALSE
## mbsub <- .getMinSub()
mbped <- mbsub[, c("famid", "id", "fatherid", "motherid", "sex")]
colnames(mbped) <- FamAgg:::.PEDCN
## using the constructor
fad <- FAData(pedigree=mbped)
##----------------------------------
## subset using boolean
fadSub <- fad[fad$family==4, ]
pedSub <- mbped[mbped$family==4, ]
pedSub$sex <- FamAgg:::sanitizeSex(pedSub$sex)
pedSub <- FamAgg:::sanitizePed(pedSub)
checkEquals(pedigree(fadSub), pedSub)
## checking kinship
kinSub <- kinship(pedigree(id=pedSub$id, dadid=pedSub$father, momid=pedSub$mother,
famid=pedSub$family, sex=as.numeric(pedSub$sex)))
checkEquals(kinship(fadSub), kinSub)
##-----------------------------------
## subset using character
ids <- c("524", "471", "17", "5", "4", "6")
pedSub <- mbped[ids, ]
pedSub$sex <- FamAgg:::sanitizeSex(pedSub$sex)
fadSub <- fad[ids, ]
## Just compare columns other than father and mother, as they have been changed!
checkEquals(pedigree(fadSub)[, c("family", "id", "sex")], pedSub[, c("family", "id", "sex")])
## kinship checking makes no sense... pedigree function does not work!
##-----------------------------------
## subset using numeric
idx <- c(4, 2, 6, 112, 12, 14)
pedSub <- mbped[idx, ]
pedSub$sex <- FamAgg:::sanitizeSex(pedSub$sex)
fadSub <- fad[idx, ]
checkEquals(pedigree(fadSub)[, c("family", "id", "sex")], pedSub[, c("family", "id", "sex")])
##-----------------------------------
## error testing
ids <- c("a", "b", "c")
checkException(fad[ids, ])
## Subset to male only:
fam4 <- fad[fad$family == "4", ]
fam4M <- fam4[fam4$sex == "M", ]
checkEquals(all(is.na(fam4M$mother)), TRUE)
if(do.plot){
## That should work.
plotPed(fam4, family="4")
## Now, how is this going to work if we've got females?
## plotPed(fam4M, family="4")
}
## manually defining the object.
fad <- new("FAData")
pedigree(fad) <- mbped
fadSub <- fad[fad$family==4, ]
pedSub <- mbped[mbped$family==4, ]
pedSub$sex <- FamAgg:::sanitizeSex(pedSub$sex)
pedSub <- FamAgg:::sanitizePed(pedSub)
checkEquals(pedigree(fadSub), pedSub)
## checking kinship
kinSub <- kinship(pedigree(id=pedSub$id, dadid=pedSub$father, momid=pedSub$mother,
famid=pedSub$family, sex=as.numeric(pedSub$sex)))
checkEquals(kinship(fadSub), kinSub)
## with age.
ages <- mbsub$endage
names(ages) <- mbped$id
fad <- FAData(pedigree=mbped, age=ages)
##-----------------------------------
## subset using boolean
fadSub <- fad[fad$family==4, ]
ageSub <- ages[mbped$family==4]
checkEquals(age(fadSub), ageSub)
##-----------------------------------
## subset using character
ids <- c("524", "471", "17", "5", "4", "6")
fadSub <- fad[ids, ]
ageSub <- ages[ids]
checkEquals(age(fadSub), ageSub)
##-----------------------------------
## subset using numeric
idx <- c(4, 2, 6, 112, 12, 14)
fadSub <- fad[idx, ]
ageSub <- ages[idx]
checkEquals(age(fadSub), ageSub)
PedDf <- mbsub[, c("famid", "id", "fatherid", "motherid", "sex")]
colnames(PedDf) <- FamAgg:::.PEDCN
tcancer <- mbsub$cancer
names(tcancer) <- mbsub$id
trait(fad) <- tcancer
## subset by boolean.
pedSub <- PedDf[PedDf$family == 5, ]
tcancerSub <- tcancer[PedDf$family == 5]
farSub <- fad[fad$family == 5, ]
checkEquals(tcancerSub, trait(farSub))
checkEquals(tcancerSub, farSub$trait)
## subset by id.
ids <- sample(rownames(pedigree(fad)), size=100)
pedSub <- PedDf[ids, ]
tcancerSub <- tcancer[ids]
farSub <- fad[ids, ]
checkEquals(tcancerSub, trait(farSub))
checkEquals(tcancerSub, farSub$trait)
## subset by idx.
idx <- sample(1:nrow(pedigree(fad)), size=100)
pedSub <- PedDf[idx, ]
tcancerSub <- tcancer[idx]
farSub <- fad[idx, ]
checkEquals(tcancerSub, trait(farSub))
checkEquals(tcancerSub, farSub$trait)
}
## testing the "sex sanitation"
test_sex_columns <- function(){
sexnum <- c(1, 1, 2, 2, 3, 1, 1, 2, 2, NA)
expect <- factor(c("M", "M", "F", "F", NA, "M", "M", "F", "F", NA),
levels=c("M", "F"))
got <- FamAgg:::sanitizeSex(sexnum)
checkEquals(got, expect)
sexchar <- c("male", "male", "female", "female", "other", "male", "Man", "female", "female", NA)
got <- FamAgg:::sanitizeSex(sexchar)
checkEquals(got, expect)
got <- FamAgg:::sanitizeSex(expect)
checkEquals(got, expect)
## now checking some errors:
checkException(FamAgg:::sanitizeSex(c(3, 2, 5, 6)))
checkException(FamAgg:::sanitizeSex(c("woman", "man", "woman", "man")))
}
## test the kinship...
test_kinship <- function(){
## mbsub <- .getMinSub()
ped <- pedigree(id=mbsub$id, dadid=mbsub$fatherid, momid=mbsub$motherid,
sex=mbsub$sex, famid=mbsub$famid)
kin <- kinship(ped)
fad <- FAData(pedigree=ped)
return(checkEquals(kin[fad$id, fad$id], kinship(fad)))
}
## testing the constructor.
test_FAData <- function(){
pedFile <- system.file("txt/minnbreastsub.txt", package="FamAgg")
checkException(fad <- FAData(pedigree=pedFile, header=TRUE))
fad <- FAData(pedigree=pedFile, header=TRUE, family.col="famid", id.col="id",
father.col="fatherid", mother.col="motherid")
mbsub <- .getMinSub()
PedDf <- mbsub[, c("famid", "id", "fatherid", "motherid", "sex")]
colnames(PedDf) <- FamAgg:::.PEDCN
PedDf$sex <- FamAgg:::sanitizeSex(PedDf$sex)
rownames(PedDf) <- as.character(PedDf$id)
PedDf <- FamAgg:::sanitizePed(PedDf)
checkEquals(PedDf, pedigree(fad))
## adding also age...
Ages <- as.numeric(mbsub$endage)
names(Ages) <- mbsub$id
fad <- FAData(pedigree=pedFile, header=TRUE, family.col="famid", id.col="id",
father.col="fatherid", mother.col="motherid", age=Ages)
checkEquals(Ages, age(fad))
Ages[1] <- 120
age(fad) <- Ages
checkEquals(Ages, age(fad))
## construct by submitting a data.frame
fad <- FAData(PedDf)
checkEquals(pedigree(fad), PedDf)
}
test_family <- function(){
## mbsub <- .getMinSub()
PedDf <- mbsub[, c("famid", "id", "fatherid", "motherid", "sex")]
colnames(PedDf) <- FamAgg:::.PEDCN
PedDf$sex <- FamAgg:::sanitizeSex(PedDf$sex)
rownames(PedDf) <- as.character(PedDf$id)
fad <- FAData(PedDf)
PedDf <- FamAgg:::sanitizePed(PedDf)
Test <- family(fad, id=7)
checkEquals(Test, PedDf[PedDf$family==4, ])
}
test_getCommonAncestor <- function(){
do.plot <- FALSE
## mbsub <- .getMinSub()
PedDf <- mbsub[, c("famid", "id", "fatherid", "motherid", "sex")]
colnames(PedDf) <- FamAgg:::.PEDCN
PedDf$sex <- FamAgg:::sanitizeSex(PedDf$sex)
rownames(PedDf) <- NULL
fad <- FAData(PedDf)
## get common ancestors for some example families
ancs <- c("759", "760")
checkEquals(sort(getCommonAncestor(fad, id=c("761", "763", "772"))), sort(ancs))
if(do.plot)
plotPed(fad, id=c("761", "763", "772"), device="plot", prune=TRUE)
##
checkException(getCommonAncestor(fad, id="761"))
checkException(getCommonAncestor(fad, id=c("761", "bla")))
}
test_buildPed <- function() {
do.plot <- FALSE
## mbsub <- .getMinSub()
PedDf <- mbsub[, c("famid", "id", "fatherid", "motherid", "sex")]
colnames(PedDf) <- FamAgg:::.PEDCN
PedDf$sex <- FamAgg:::sanitizeSex(PedDf$sex)
rownames(PedDf) <- NULL
fad <- FAData(PedDf)
if(do.plot){
switchPlotfun("ks2paint")
plotPed(fad, id="4", device="plot")
switchPlotfun()
}
tmpf <- paste0(tempfile(), ".tsv")
switchPlotfun("haplopaint", check=FALSE)
plotPed(fad, id="4", device="txt")
switchPlotfun("ks2paint")
file.remove(tmpf)
expect <- c(5, 26, 11, 12, 13)
tmp <- buildPed(fad, id = c(26, 13, 12, 11), prune = TRUE)
checkEquals(sort(tmp$id), sort(expect))
expect <- c(23, 3, 24, 4, 25, 5, 26, 11, 1, 2)
tmp <- buildPed(fad, id = c(23, 11), prune = TRUE)
checkEquals(sort(tmp$id), sort(expect))
## build ped for individuals of family 14:
## pedigree for individual 447 should include individuals of a second
## branch, e.g. individual 26062
checkTrue(any(buildPed(fad, id = "447")$id == "26062"))
## for individual 440 (father of 447) this second branch should be
## missing
checkTrue(!any(buildPed(fad, id = "440")$id == "26062"))
checkException(buildPed(fad, family = 2))
res <- buildPed(fad, family = "5")
res_2 <- family(fad, family = "5")
checkTrue(nrow(res) < nrow(res_2))
res_2 <- removeSingletons(res_2)
res_2 <- res_2[order(res_2$id), ]
res <- res[order(res$id), ]
checkEquals(res, res_2)
}
test_dollar <- function(){
mbped <- mbsub[, c("famid", "id", "fatherid", "motherid", "sex")]
colnames(mbped) <- FamAgg:::.PEDCN
far <- FAData(pedigree=mbped)
tcancer <- mbsub$cancer
names(tcancer) <- mbsub$id
trait(far) <- tcancer
checkEquals(far$affected, tcancer)
## basic stuff from pedigree...
ids <- as.character(pedigree(far)$id)
names(ids) <- as.character(ids)
checkEquals(far$id, ids)
## family
tmp <- pedigree(far)$family
names(tmp) <- as.character(pedigree(far)$id)
checkEquals(far$family, tmp)
## father
tmp <- pedigree(far)$father
names(tmp) <- as.character(pedigree(far)$id)
checkEquals(far$father, tmp)
## mother
tmp <- pedigree(far)$mother
names(tmp) <- as.character(pedigree(far)$id)
checkEquals(far$mother, tmp)
}
## Here we just want to ensure that it's OK to have either 0 or NA for founders in
## the pedigree.
test_kinship2_kinship <- function(){
mbped <- mbsub[, c("famid", "id", "fatherid", "motherid", "sex")]
colnames(mbped) <- FamAgg:::.PEDCN
pediNumeric <- pedigree(id=mbped$id, famid=mbped$family, dadid=mbped$father,
momid=mbped$mother, sex=mbped$sex)
kinNumeric <- kinship(pediNumeric)
## Replacing 0s with NAs:
mbped$father[mbped$father == 0] <- NA
mbped$mother[mbped$mother == 0] <- NA
pediNumericNA <- pedigree(id=mbped$id, famid=mbped$family, dadid=mbped$father,
momid=mbped$mother, sex=mbped$sex)
kinNumericNA <- kinship(pediNumeric)
checkEquals(kinNumeric, kinNumericNA)
## And now character:
mbped$id <- as.character(mbped$id)
mbped$father <- as.character(mbped$father)
mbped$mother <- as.character(mbped$mother)
pediCharNA <- pedigree(id=mbped$id, famid=mbped$family, dadid=mbped$father,
momid=mbped$mother, sex=mbped$sex)
kinCharNA <- kinship(pediCharNA)
checkEquals(kinNumeric, kinCharNA)
## The same but with "0" for founders.
mbped$father[is.na(mbped$father)] <- 0
mbped$mother[is.na(mbped$mother)] <- 0
checkException(pedigree(id=mbped$id, famid=mbped$family, dadid=mbped$father,
momid=mbped$mother, sex=mbped$sex))
## "" for "0"
mbped$father[mbped$father == "0"] <- ""
mbped$mother[mbped$mother == "0"] <- ""
pediCharZ <- pedigree(id=mbped$id, famid=mbped$family, dadid=mbped$father,
momid=mbped$mother, sex=mbped$sex)
kinCharZ <- kinship(pediCharZ)
checkEquals(kinNumeric, kinCharZ)
}
test_export <- function(){
mbped <- mbsub[, c("famid", "id", "fatherid", "motherid", "sex")]
colnames(mbped) <- FamAgg:::.PEDCN
far <- FAData(pedigree=mbped)
fam4 <- far[far$family == 4, ]
tmpF <- paste0(tempfile(), ".ped")
export(fam4, tmpF, format="ped")
fam4imported <- FAData(tmpF)
checkEquals(as.character(pedigree(fam4)$family), pedigree(fam4imported)$family)
checkEquals(as.character(pedigree(fam4)$id), pedigree(fam4imported)$id)
checkEquals(as.character(pedigree(fam4)$father), pedigree(fam4imported)$father)
checkEquals(as.character(pedigree(fam4)$mother), pedigree(fam4imported)$mother)
checkEquals(as.character(pedigree(fam4)$sex), as.character(pedigree(fam4imported)$sex))
}
test_genevieve_reported_errors <- function() {
ped <- data.frame(family = c("a", "a", "a", "a", "b", "b", "b"),
id = c(1, 2, 3, 4, 1, 2, 3),
father = c(0, 0, 1, 1, 0, 0, 1),
mother = c(0, 0, 2, 2, 0, 0, 2),
sex = c("M", "F", "M", "F", "M", "F", "F"),
stringsAsFactors = FALSE)
checkException(FAData(ped))
## Combine family and id
ped2 <- ped
ped2$id <- paste0(ped$family, "-", ped$id)
ped2$father <- paste0(ped$family, "-", ped$father)
ped2$mother <- paste0(ped$family, "-", ped$mother)
## Fixing the founder
ped2$father[ped$father == 0] <- NA
ped2$mother[ped$mother == 0] <- NA
fad <- FAData(ped2)
ped3 <- ped
ped3$id <- paste0(ped$family, "-", ped$id)
ped3$father <- paste0(ped$family, "-", ped$father)
ped3$mother <- paste0(ped$family, "-", ped$mother)
## Fixing the founder
ped3$father[ped$father == 0] <- 0
ped3$mother[ped$mother == 0] <- 0
fad <- FAData(ped3)
}
EuracBiomedicalResearch/FamAgg documentation built on March 12, 2023, 7:45 p.m.
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.getMinSub <- function(){
data(minnbreast)
mbsub <- minnbreast[minnbreast$famid %in% 4:19, ]
return(mbsub)
}
mbsub <- .getMinSub()
test_show <- function() {
mbped <- mbsub[, c("famid", "id", "fatherid", "motherid", "sex")]
colnames(mbped) <- FamAgg:::.PEDCN
fad <- FAData(pedigree=mbped)
res <- capture.output(show(fad))
checkEquals(res[1], "FAData object with:")
}
test_construct <- function(){
mbped <- mbsub[, c("famid", "id", "fatherid", "motherid", "sex")]
colnames(mbped) <- FamAgg:::.PEDCN
fad <- FAData(pedigree=mbped)
tcancer <- mbsub$cancer
names(tcancer) <- mbsub$id
trait(fad) <- tcancer
## constructor with the trait
fad <- FAData(pedigree=mbped, trait=mbsub$cancer)
tcancershuffle <- sample(tcancer, length(tcancer))
trait(fad) <- tcancershuffle
## the function internally has to rematch the ids
checkEquals(trait(fad), tcancer)
## testing the $ accessor
checkEquals(fad$trait, tcancer)
fad@traitname <- "cancer"
checkEquals(fad$cancer, tcancer)
## check if the pedigree returns the correct extended pedigree
## with the additional column affected
ped <- pedigree(fad)
fromPed <- ped$affected
names(fromPed) <- ped$id
checkEquals(fromPed, tcancer)
## test affected and phenotyped individuals
affIds <- affectedIndividuals(fad)
checkEquals(affIds, as.character(ped$id[which(ped$affected == 1)]))
phenoIds <- phenotypedIndividuals(fad)
checkEquals(phenoIds, as.character(ped$id[!is.na(ped$affected)]))
## check if a logical trait is handled properly
tcancerrandom <- sample(c(rep(T, 3), rep(F, 7), NA), size=length(tcancer),
replace = TRUE)
names(tcancerrandom) <- names(tcancer)
fad1 <- FAData(pedigree=mbped, trait=tcancerrandom)
fad2 <- FAData(pedigree=mbped)
trait(fad2) <- tcancerrandom
checkEquals(trait(fad1), trait(fad2))
tcint <- as.integer(tcancerrandom)
names(tcint) <- names(tcancerrandom)
checkEquals(trait(fad1), tcint)
}
test_FAData_from_file <- function(){
## create from file
pedfile <- system.file("txt/minnbreastsub.txt", package="FamAgg")
checkException(fad2 <- FAData(pedfile, id.col="ID" ))
fad2 <- FAData(pedfile, id.col="id", family.col="famid", father.col="fatherid",
mother.col="motherid", sex.col="sex", header=TRUE)
## Now read it from ped
pedfile <- system.file("txt/minnbreastsub.ped.gz", package="FamAgg")
fadPed <- FAData(pedfile)
pedfile <- system.file("txt/minnbreastsub-bad.ped.gz", package="FamAgg")
checkException(FAData(pedfile))
}
## Testing the validation methods
test_validate <- function(){
tmpPed <- mbsub[, c("famid", "id", "fatherid", "motherid", "sex")]
colnames(tmpPed) <- FamAgg:::.PEDCN
## Don't allow NAs in id, father or mother
badPed <- tmpPed
badPed[13, "id"] <- NA
checkException(FAData(badPed))
badPed <- tmpPed
badPed[13, "father"] <- NA
checkException(FAData(badPed))
badPed <- tmpPed
badPed[13, "mother"] <- NA
checkException(FAData(badPed))
## Don't allow father or mother ids other than 0 or %in% $id
badPed <- tmpPed
badPed[13, "mother"] <- "123345"
checkException(FAData(badPed))
badPed <- tmpPed
badPed[13, "father"] <- "123345"
checkException(FAData(badPed))
}
## OK, 0.0.6
test_age <- function(){
mbped <- mbsub[, c("famid", "id", "fatherid", "motherid", "sex")]
colnames(mbped) <- FamAgg:::.PEDCN
tmp <- new("FAData")
ages <- mbsub$endage
names(ages) <- mbped$id
## Setting ages to a empty object should not add age.
age(tmp) <- ages
checkEquals(length(age(tmp)), 0)
checkTrue(validObject(tmp))
## With pedigree:
pedigree(tmp) <- mbped
checkTrue(validObject(tmp))
age(tmp) <- ages
checkEqualsNumeric(length(age(tmp)), length(ages))
checkEqualsNumeric(length(age(tmp)), nrow(mbped))
checkEquals(names(age(tmp)), as.character(mbped[, 2]))
}
test_pedigree <- function(){
tmp <- new("FAData")
## mbsub <- .getMinSub()
PedDf <- mbsub[, c("famid", "id", "fatherid", "motherid", "sex")]
colnames(PedDf) <- FamAgg:::.PEDCN
pedigree(tmp) <- PedDf
checkTrue(is(pedigree(tmp, return.type="data.frame"), "data.frame"))
tmp2 <- pedigree(tmp, return.type="data.frame")
## have to transform sex into a factor...
PedDf$sex <- factor(PedDf$sex, levels=c("M", "F"))
rownames(PedDf) <- as.character(PedDf$id)
checkEquals(tmp2, FamAgg:::sanitizePed(PedDf))
## submit a pedigree(List) object...
Ped <- pedigree(id=PedDf[, 2], famid=PedDf[, 1], dadid=PedDf[, 3],
momid=PedDf[, 4], sex=PedDf[, 5])
pedigree(tmp) <- Ped
checkTrue(is(pedigree(tmp, return.type="pedigree"), "pedigreeList"))
## check the Ped with the pedigree(tmp)
tmp1 <- do.call(cbind, Ped)
tmp2 <- do.call(cbind, pedigree(tmp, return.type="pedigree"))
checkEquals(tmp1, tmp2)
}
test_subset <- function(){
do.plot <- FALSE
## mbsub <- .getMinSub()
mbped <- mbsub[, c("famid", "id", "fatherid", "motherid", "sex")]
colnames(mbped) <- FamAgg:::.PEDCN
## using the constructor
fad <- FAData(pedigree=mbped)
##----------------------------------
## subset using boolean
fadSub <- fad[fad$family==4, ]
pedSub <- mbped[mbped$family==4, ]
pedSub$sex <- FamAgg:::sanitizeSex(pedSub$sex)
pedSub <- FamAgg:::sanitizePed(pedSub)
checkEquals(pedigree(fadSub), pedSub)
## checking kinship
kinSub <- kinship(pedigree(id=pedSub$id, dadid=pedSub$father, momid=pedSub$mother,
famid=pedSub$family, sex=as.numeric(pedSub$sex)))
checkEquals(kinship(fadSub), kinSub)
##-----------------------------------
## subset using character
ids <- c("524", "471", "17", "5", "4", "6")
pedSub <- mbped[ids, ]
pedSub$sex <- FamAgg:::sanitizeSex(pedSub$sex)
fadSub <- fad[ids, ]
## Just compare columns other than father and mother, as they have been changed!
checkEquals(pedigree(fadSub)[, c("family", "id", "sex")], pedSub[, c("family", "id", "sex")])
## kinship checking makes no sense... pedigree function does not work!
##-----------------------------------
## subset using numeric
idx <- c(4, 2, 6, 112, 12, 14)
pedSub <- mbped[idx, ]
pedSub$sex <- FamAgg:::sanitizeSex(pedSub$sex)
fadSub <- fad[idx, ]
checkEquals(pedigree(fadSub)[, c("family", "id", "sex")], pedSub[, c("family", "id", "sex")])
##-----------------------------------
## error testing
ids <- c("a", "b", "c")
checkException(fad[ids, ])
## Subset to male only:
fam4 <- fad[fad$family == "4", ]
fam4M <- fam4[fam4$sex == "M", ]
checkEquals(all(is.na(fam4M$mother)), TRUE)
if(do.plot){
## That should work.
plotPed(fam4, family="4")
## Now, how is this going to work if we've got females?
## plotPed(fam4M, family="4")
}
## manually defining the object.
fad <- new("FAData")
pedigree(fad) <- mbped
fadSub <- fad[fad$family==4, ]
pedSub <- mbped[mbped$family==4, ]
pedSub$sex <- FamAgg:::sanitizeSex(pedSub$sex)
pedSub <- FamAgg:::sanitizePed(pedSub)
checkEquals(pedigree(fadSub), pedSub)
## checking kinship
kinSub <- kinship(pedigree(id=pedSub$id, dadid=pedSub$father, momid=pedSub$mother,
famid=pedSub$family, sex=as.numeric(pedSub$sex)))
checkEquals(kinship(fadSub), kinSub)
## with age.
ages <- mbsub$endage
names(ages) <- mbped$id
fad <- FAData(pedigree=mbped, age=ages)
##-----------------------------------
## subset using boolean
fadSub <- fad[fad$family==4, ]
ageSub <- ages[mbped$family==4]
checkEquals(age(fadSub), ageSub)
##-----------------------------------
## subset using character
ids <- c("524", "471", "17", "5", "4", "6")
fadSub <- fad[ids, ]
ageSub <- ages[ids]
checkEquals(age(fadSub), ageSub)
##-----------------------------------
## subset using numeric
idx <- c(4, 2, 6, 112, 12, 14)
fadSub <- fad[idx, ]
ageSub <- ages[idx]
checkEquals(age(fadSub), ageSub)
PedDf <- mbsub[, c("famid", "id", "fatherid", "motherid", "sex")]
colnames(PedDf) <- FamAgg:::.PEDCN
tcancer <- mbsub$cancer
names(tcancer) <- mbsub$id
trait(fad) <- tcancer
## subset by boolean.
pedSub <- PedDf[PedDf$family == 5, ]
tcancerSub <- tcancer[PedDf$family == 5]
farSub <- fad[fad$family == 5, ]
checkEquals(tcancerSub, trait(farSub))
checkEquals(tcancerSub, farSub$trait)
## subset by id.
ids <- sample(rownames(pedigree(fad)), size=100)
pedSub <- PedDf[ids, ]
tcancerSub <- tcancer[ids]
farSub <- fad[ids, ]
checkEquals(tcancerSub, trait(farSub))
checkEquals(tcancerSub, farSub$trait)
## subset by idx.
idx <- sample(1:nrow(pedigree(fad)), size=100)
pedSub <- PedDf[idx, ]
tcancerSub <- tcancer[idx]
farSub <- fad[idx, ]
checkEquals(tcancerSub, trait(farSub))
checkEquals(tcancerSub, farSub$trait)
}
## testing the "sex sanitation"
test_sex_columns <- function(){
sexnum <- c(1, 1, 2, 2, 3, 1, 1, 2, 2, NA)
expect <- factor(c("M", "M", "F", "F", NA, "M", "M", "F", "F", NA),
levels=c("M", "F"))
got <- FamAgg:::sanitizeSex(sexnum)
checkEquals(got, expect)
sexchar <- c("male", "male", "female", "female", "other", "male", "Man", "female", "female", NA)
got <- FamAgg:::sanitizeSex(sexchar)
checkEquals(got, expect)
got <- FamAgg:::sanitizeSex(expect)
checkEquals(got, expect)
## now checking some errors:
checkException(FamAgg:::sanitizeSex(c(3, 2, 5, 6)))
checkException(FamAgg:::sanitizeSex(c("woman", "man", "woman", "man")))
}
## test the kinship...
test_kinship <- function(){
## mbsub <- .getMinSub()
ped <- pedigree(id=mbsub$id, dadid=mbsub$fatherid, momid=mbsub$motherid,
sex=mbsub$sex, famid=mbsub$famid)
kin <- kinship(ped)
fad <- FAData(pedigree=ped)
return(checkEquals(kin[fad$id, fad$id], kinship(fad)))
}
## testing the constructor.
test_FAData <- function(){
pedFile <- system.file("txt/minnbreastsub.txt", package="FamAgg")
checkException(fad <- FAData(pedigree=pedFile, header=TRUE))
fad <- FAData(pedigree=pedFile, header=TRUE, family.col="famid", id.col="id",
father.col="fatherid", mother.col="motherid")
mbsub <- .getMinSub()
PedDf <- mbsub[, c("famid", "id", "fatherid", "motherid", "sex")]
colnames(PedDf) <- FamAgg:::.PEDCN
PedDf$sex <- FamAgg:::sanitizeSex(PedDf$sex)
rownames(PedDf) <- as.character(PedDf$id)
PedDf <- FamAgg:::sanitizePed(PedDf)
checkEquals(PedDf, pedigree(fad))
## adding also age...
Ages <- as.numeric(mbsub$endage)
names(Ages) <- mbsub$id
fad <- FAData(pedigree=pedFile, header=TRUE, family.col="famid", id.col="id",
father.col="fatherid", mother.col="motherid", age=Ages)
checkEquals(Ages, age(fad))
Ages[1] <- 120
age(fad) <- Ages
checkEquals(Ages, age(fad))
## construct by submitting a data.frame
fad <- FAData(PedDf)
checkEquals(pedigree(fad), PedDf)
}
test_family <- function(){
## mbsub <- .getMinSub()
PedDf <- mbsub[, c("famid", "id", "fatherid", "motherid", "sex")]
colnames(PedDf) <- FamAgg:::.PEDCN
PedDf$sex <- FamAgg:::sanitizeSex(PedDf$sex)
rownames(PedDf) <- as.character(PedDf$id)
fad <- FAData(PedDf)
PedDf <- FamAgg:::sanitizePed(PedDf)
Test <- family(fad, id=7)
checkEquals(Test, PedDf[PedDf$family==4, ])
}
test_getCommonAncestor <- function(){
do.plot <- FALSE
## mbsub <- .getMinSub()
PedDf <- mbsub[, c("famid", "id", "fatherid", "motherid", "sex")]
colnames(PedDf) <- FamAgg:::.PEDCN
PedDf$sex <- FamAgg:::sanitizeSex(PedDf$sex)
rownames(PedDf) <- NULL
fad <- FAData(PedDf)
## get common ancestors for some example families
ancs <- c("759", "760")
checkEquals(sort(getCommonAncestor(fad, id=c("761", "763", "772"))), sort(ancs))
if(do.plot)
plotPed(fad, id=c("761", "763", "772"), device="plot", prune=TRUE)
##
checkException(getCommonAncestor(fad, id="761"))
checkException(getCommonAncestor(fad, id=c("761", "bla")))
}
test_buildPed <- function() {
do.plot <- FALSE
## mbsub <- .getMinSub()
PedDf <- mbsub[, c("famid", "id", "fatherid", "motherid", "sex")]
colnames(PedDf) <- FamAgg:::.PEDCN
PedDf$sex <- FamAgg:::sanitizeSex(PedDf$sex)
rownames(PedDf) <- NULL
fad <- FAData(PedDf)
if(do.plot){
switchPlotfun("ks2paint")
plotPed(fad, id="4", device="plot")
switchPlotfun()
}
tmpf <- paste0(tempfile(), ".tsv")
switchPlotfun("haplopaint", check=FALSE)
plotPed(fad, id="4", device="txt")
switchPlotfun("ks2paint")
file.remove(tmpf)
expect <- c(5, 26, 11, 12, 13)
tmp <- buildPed(fad, id = c(26, 13, 12, 11), prune = TRUE)
checkEquals(sort(tmp$id), sort(expect))
expect <- c(23, 3, 24, 4, 25, 5, 26, 11, 1, 2)
tmp <- buildPed(fad, id = c(23, 11), prune = TRUE)
checkEquals(sort(tmp$id), sort(expect))
## build ped for individuals of family 14:
## pedigree for individual 447 should include individuals of a second
## branch, e.g. individual 26062
checkTrue(any(buildPed(fad, id = "447")$id == "26062"))
## for individual 440 (father of 447) this second branch should be
## missing
checkTrue(!any(buildPed(fad, id = "440")$id == "26062"))
checkException(buildPed(fad, family = 2))
res <- buildPed(fad, family = "5")
res_2 <- family(fad, family = "5")
checkTrue(nrow(res) < nrow(res_2))
res_2 <- removeSingletons(res_2)
res_2 <- res_2[order(res_2$id), ]
res <- res[order(res$id), ]
checkEquals(res, res_2)
}
test_dollar <- function(){
mbped <- mbsub[, c("famid", "id", "fatherid", "motherid", "sex")]
colnames(mbped) <- FamAgg:::.PEDCN
far <- FAData(pedigree=mbped)
tcancer <- mbsub$cancer
names(tcancer) <- mbsub$id
trait(far) <- tcancer
checkEquals(far$affected, tcancer)
## basic stuff from pedigree...
ids <- as.character(pedigree(far)$id)
names(ids) <- as.character(ids)
checkEquals(far$id, ids)
## family
tmp <- pedigree(far)$family
names(tmp) <- as.character(pedigree(far)$id)
checkEquals(far$family, tmp)
## father
tmp <- pedigree(far)$father
names(tmp) <- as.character(pedigree(far)$id)
checkEquals(far$father, tmp)
## mother
tmp <- pedigree(far)$mother
names(tmp) <- as.character(pedigree(far)$id)
checkEquals(far$mother, tmp)
}
## Here we just want to ensure that it's OK to have either 0 or NA for founders in
## the pedigree.
test_kinship2_kinship <- function(){
mbped <- mbsub[, c("famid", "id", "fatherid", "motherid", "sex")]
colnames(mbped) <- FamAgg:::.PEDCN
pediNumeric <- pedigree(id=mbped$id, famid=mbped$family, dadid=mbped$father,
momid=mbped$mother, sex=mbped$sex)
kinNumeric <- kinship(pediNumeric)
## Replacing 0s with NAs:
mbped$father[mbped$father == 0] <- NA
mbped$mother[mbped$mother == 0] <- NA
pediNumericNA <- pedigree(id=mbped$id, famid=mbped$family, dadid=mbped$father,
momid=mbped$mother, sex=mbped$sex)
kinNumericNA <- kinship(pediNumeric)
checkEquals(kinNumeric, kinNumericNA)
## And now character:
mbped$id <- as.character(mbped$id)
mbped$father <- as.character(mbped$father)
mbped$mother <- as.character(mbped$mother)
pediCharNA <- pedigree(id=mbped$id, famid=mbped$family, dadid=mbped$father,
momid=mbped$mother, sex=mbped$sex)
kinCharNA <- kinship(pediCharNA)
checkEquals(kinNumeric, kinCharNA)
## The same but with "0" for founders.
mbped$father[is.na(mbped$father)] <- 0
mbped$mother[is.na(mbped$mother)] <- 0
checkException(pedigree(id=mbped$id, famid=mbped$family, dadid=mbped$father,
momid=mbped$mother, sex=mbped$sex))
## "" for "0"
mbped$father[mbped$father == "0"] <- ""
mbped$mother[mbped$mother == "0"] <- ""
pediCharZ <- pedigree(id=mbped$id, famid=mbped$family, dadid=mbped$father,
momid=mbped$mother, sex=mbped$sex)
kinCharZ <- kinship(pediCharZ)
checkEquals(kinNumeric, kinCharZ)
}
test_export <- function(){
mbped <- mbsub[, c("famid", "id", "fatherid", "motherid", "sex")]
colnames(mbped) <- FamAgg:::.PEDCN
far <- FAData(pedigree=mbped)
fam4 <- far[far$family == 4, ]
tmpF <- paste0(tempfile(), ".ped")
export(fam4, tmpF, format="ped")
fam4imported <- FAData(tmpF)
checkEquals(as.character(pedigree(fam4)$family), pedigree(fam4imported)$family)
checkEquals(as.character(pedigree(fam4)$id), pedigree(fam4imported)$id)
checkEquals(as.character(pedigree(fam4)$father), pedigree(fam4imported)$father)
checkEquals(as.character(pedigree(fam4)$mother), pedigree(fam4imported)$mother)
checkEquals(as.character(pedigree(fam4)$sex), as.character(pedigree(fam4imported)$sex))
}
test_genevieve_reported_errors <- function() {
ped <- data.frame(family = c("a", "a", "a", "a", "b", "b", "b"),
id = c(1, 2, 3, 4, 1, 2, 3),
father = c(0, 0, 1, 1, 0, 0, 1),
mother = c(0, 0, 2, 2, 0, 0, 2),
sex = c("M", "F", "M", "F", "M", "F", "F"),
stringsAsFactors = FALSE)
checkException(FAData(ped))
## Combine family and id
ped2 <- ped
ped2$id <- paste0(ped$family, "-", ped$id)
ped2$father <- paste0(ped$family, "-", ped$father)
ped2$mother <- paste0(ped$family, "-", ped$mother)
## Fixing the founder
ped2$father[ped$father == 0] <- NA
ped2$mother[ped$mother == 0] <- NA
fad <- FAData(ped2)
ped3 <- ped
ped3$id <- paste0(ped$family, "-", ped$id)
ped3$father <- paste0(ped$family, "-", ped$father)
ped3$mother <- paste0(ped$family, "-", ped$mother)
## Fixing the founder
ped3$father[ped$father == 0] <- 0
ped3$mother[ped$mother == 0] <- 0
fad <- FAData(ped3)
}
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