/usr/lib/R/site-library/IRanges/unitTests/test_RDApplyParams.R is in r-bioc-iranges 2.4.1-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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fun <- function(rd) NULL
ranges <- IRanges(c(1,2,3),c(4,5,6))
filter <- c(1L, 0L, 1L)
applyParams <- list(x = 2)
excludePattern <- "[XY]"
rd <- RangedData(ranges, filter)
## meaningless defaults
checkTrue(validObject(RDApplyParams()))
checkTrue(validObject(RDApplyParams(rd)))
## finally does something
params <- RDApplyParams(rd, fun)
checkTrue(validObject(params))
checkIdentical(rangedData(params), rd)
checkIdentical(applyFun(params), fun)
## make sure function and parameters compatible
## applyFun needs 1 param
checkException(applyFun(params) <- function() NULL, silent = TRUE)
checkException(RDApplyParams(rd, function() NULL), silent = TRUE)
## needs 2 params
checkException(RDApplyParams(rd, fun, applyParams), silent = TRUE)
checkException(applyParams(params) <- applyParams, silent = TRUE)
## parameter name mismatch
checkException(RDApplyParams(rd, function(rd, y) NULL, applyParams),
silent = TRUE)
applyFun(params) <- function(rd, y) NULL
checkTrue(validObject(params))
checkException(applyParams(params) <- applyParams, silent = TRUE)
## ok with ...
applyFun(params) <- function(...) NULL
checkTrue(validObject(params))
checkIdentical(applyFun(params), function(...) NULL)
applyParams(params) <- applyParams
checkTrue(validObject(params))
checkIdentical(applyParams(params), applyParams)
params <- RDApplyParams(rd, function(...) NULL, applyParams)
checkTrue(validObject(params))
checkIdentical(applyParams(params), applyParams)
## check for duplicate params
checkException(applyParams(params) <- rep(applyParams,2), silent = TRUE)
checkException(RDApplyParams(rd, function(...) NULL, rep(applyParams,2)),
silent = TRUE)
## exclude pattern -- length 1 character vector
## excludePattern(params) <- excludePattern
## checkTrue(validObject(params))
## checkIdentical(excludePattern(params), excludePattern)
## params <- RDApplyParams(rd, function(...) NULL,
## excludePattern = excludePattern)
## checkTrue(validObject(params))
## checkIdentical(excludePattern(params), excludePattern)
## checkException(RDApplyParams(rd, function(...) NULL,
## excludePattern = rep(excludePattern,2)))
## checkExcpetion(excludePattern(params)) <- rep(excludePattern, 2)
## filters
filterRules <- FilterRules()
filterRules(params) <- filterRules
checkIdentical(filterRules(params), filterRules)
params <- RDApplyParams(rd, function(...) NULL, filterRules = filterRules)
checkTrue(validObject(params))
checkIdentical(filterRules(params), filterRules)
filterRules <- FilterRules(list(basic = "filter",
advanced = function(rd) NULL))
filterRules(params) <- filterRules
checkTrue(validObject(params))
## simplify -- length 1 logical
simplify(params) <- TRUE
checkTrue(validObject(params))
checkIdentical(simplify(params), TRUE)
params <- RDApplyParams(rd, function(...) NULL, simplify = TRUE)
checkTrue(validObject(params))
checkIdentical(simplify(params), TRUE)
checkException(RDApplyParams(rd, function(...) NULL,
simplify = rep(TRUE,2)), silent = TRUE)
checkException(simplify(params) <- rep(FALSE, 2), silent = TRUE)
## reducer
reducer <- function(rd) NULL
## oops, simplify is TRUE
checkException(reducerFun(params) <- reducer, silent = TRUE)
checkException(RDApplyParams(rd, function(...) NULL, simplify = TRUE,
reducerFun = reducer), silent = TRUE)
simplify(params) <- FALSE
reducerFun(params) <- reducer
checkTrue(validObject(params))
checkIdentical(reducerFun(params), reducer)
params <- RDApplyParams(rd, function(...) NULL, reducerFun = reducer)
checkTrue(validObject(params))
checkIdentical(reducerFun(params), reducer)
reducerFun(params) <- NULL ## don't reduce
checkTrue(validObject(params))
checkIdentical(reducerFun(params), NULL)
## reducer params
## NOTE: for some reason, new() becomes confused if we use 'applyParams' here
reducerParams <- applyParams
checkException(RDApplyParams(rd, function(...) NULL, ## oops, no reducer
reducerParams = reducerParams), silent = TRUE)
checkException(reducerParams(params) <- reducerParams, silent = TRUE)
## conflicts between reducer and its params
## needs 1 param
checkException(reducerFun(params) <- function() NULL, silent = TRUE)
checkException(RDApplyParams(rd, reducerFun = function() NULL), silent = TRUE)
checkException(RDApplyParams(rd, fun, reducerFun = reducer,
reducerParams = reducerParams),
silent = TRUE) # needs 2 params
reducerFun(params) <- function(rd) NULL
checkException(reducerParams(params) <- reducerParams, silent = TRUE)
## parameter name mismatch
checkException(RDApplyParams(rd, function(rd) NULL,
reducerFun = function(rd, y) NULL,
reducerParams = reducerParams), silent = TRUE)
reducerFun(params) <- function(rd, y) NULL
checkTrue(validObject(params))
checkException(reducerParams(params) <- reducerParams, silent = TRUE)
## ok with ...
reducerFun(params) <- function(...) NULL
checkTrue(validObject(params))
checkIdentical(reducerFun(params), function(...) NULL)
reducerParams(params) <- reducerParams
checkTrue(validObject(params))
checkIdentical(reducerParams(params), reducerParams)
params <- RDApplyParams(rd, function(rd) NULL,
reducerFun = function(...) NULL,
reducerParams = reducerParams)
checkTrue(validObject(params))
checkIdentical(reducerParams(params), reducerParams)
checkException(reducerParams(params) <- rep(reducerParams,2), silent = TRUE)
checkException(reducerParams(params) <- rep(reducerParams,2), silent = TRUE)
checkException(RDApplyParams(rd, function(...) NULL, reducerFun = reducer,
reducerParams = rep(reducerParams,2)),
silent = TRUE)
## iteratorFun
params <- RDApplyParams(rd, iteratorFun = lapply)
checkTrue(validObject(params))
checkIdentical(iteratorFun(params), lapply)
iteratorFun(params) <- sapply
checkTrue(validObject(params))
checkIdentical(iteratorFun(params), sapply)
checkException(iteratorFun(params) <- function(x) NULL, silent=TRUE)
checkException(iteratorFun(params) <- function(x, simplify) NULL, silent=TRUE)
}
test_RDApplyParams_rdapply <- function() {
ranges <- IRanges(c(1,2,3),c(4,5,6))
filter <- c(2L, 0L, 1L)
rd <- RangedData(ranges, filter, space = c("chr1","chr2","chr1"))
fun <- function(rd) NULL
countrows <- function(rd) nrow(rd)
applyParams <- list(x = 2)
excludePattern <- "[XY]"
## a single function
params <- RDApplyParams(rd, fun)
checkIdentical(rdapply(params), list(chr1 = NULL, chr2 = NULL))
## with a parameter
params <- RDApplyParams(rd, function(rd, x) x, list(x = 2))
checkIdentical(rdapply(params), list(chr1 = 2, chr2 = 2))
## add a filter
cutoff <- 0
cutoffFun <- function(rd) rd[["filter"]] > cutoff
rules <- FilterRules(list(filter = cutoffFun))
params <- RDApplyParams(rd, countrows, filterRules = rules)
checkIdentical(rdapply(params), list(chr1 = 2L, chr2 = 0L))
rules <- FilterRules(list(fun = function(rd) rd[["filter"]] < 2,
filter = cutoffFun))
params <- RDApplyParams(rd, countrows, filterRules = rules)
checkIdentical(rdapply(params), list(chr1 = 1L, chr2 = 0L))
active(filterRules(params))["filter"] <- FALSE
checkIdentical(rdapply(params), list(chr1 = 1L, chr2 = 1L))
## simplify
params <- RDApplyParams(rd, countrows, simplify = TRUE)
checkIdentical(rdapply(params), c(chr1 = 2L, chr2 = 1L))
## reducing
params <- RDApplyParams(rd, fun, reducerFun = unlist)
checkIdentical(rdapply(params), NULL)
params <- RDApplyParams(rd, countrows, reducerFun = unlist,
reducerParams = list(use.names = FALSE))
checkIdentical(rdapply(params), c(2L, 1L))
}
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