inst/unitTests/test_IRangesList-class.R

In Bioconductor/IRanges: Foundation of integer range manipulation in Bioconductor

test_IRangesList_construction <- function() {
  range1 <- IRanges(start=c(1,2,3), end=c(5,2,8))
  range2 <- IRanges(start=c(15,45,20,1), end=c(15,100,80,5))
  for (compress in c(TRUE, FALSE)) {
    empty <- IRangesList(compress=compress)
    checkTrue(validObject(empty))
    checkIdentical(length(empty), 0L)
    named <- IRangesList(one = range1, two = range2, compress=compress)
    checkTrue(validObject(named))
    checkIdentical(length(named), 2L)
    checkIdentical(start(named),
                   IntegerList(one = start(range1), two = start(range2),
                               compress=compress))
    checkIdentical(end(named),
                   IntegerList(one = end(range1), two = end(range2),
                               compress=compress))
    checkIdentical(width(named),
                   IntegerList(one = width(range1), two = width(range2),
                               compress=compress))
    checkIdentical(names(named), c("one", "two"))
    checkIdentical(range1, named[[1]])
    unnamed <- IRangesList(range1, range2, compress=compress)
    checkTrue(validObject(unnamed))
    checkIdentical(length(unnamed), 2L)
    checkIdentical(range2, unnamed[[2]])
    checkIdentical(names(unnamed), NULL)
  }
}

test_IRangesList_subset <- function() {
  for (compress in c(TRUE, FALSE)) {
    range1 <- IRanges(start=c(1,2,3), end=c(5,2,8))
    range2 <- IRanges(start=c(1,15,20,45), end=c(5,15,100,80))
    collection <- IRangesList(one = range1, range2, compress=compress)
    checkIdentical(subsetByOverlaps(collection, IRangesList()),
                   IRangesList(one=IRanges(), IRanges(), compress=compress))
    checkIdentical(
      subsetByOverlaps(collection,
                       IRangesList(IRanges(4, 6), IRanges(50, 70),
                                   compress=compress)),
                       IRangesList(one=IRanges(c(1,3),c(5,8)),
                                   IRanges(c(20,45),c(100,80)),
                                   compress=compress))
    checkIdentical(
      subsetByOverlaps(collection,
                       IRangesList(IRanges(50, 70), one=IRanges(4, 6),
                                   compress=compress)),
                       IRangesList(one=IRanges(c(1,3),c(5,8)), IRanges(),
                                   compress=compress))
  }
}

test_IRangesList_as_list <- function() {
  for (compress in c(TRUE, FALSE)) {
    range1 <- IRanges(start=c(1,2,3), end=c(5,2,8))
    range2 <- IRanges(start=c(15,45,20,1), end=c(15,100,80,5))
    checkIdentical(list(range1, range2),
                   as.list(IRangesList(range1, range2, compress=compress)))
    checkIdentical(list(a=range1, b=range2),
                   as.list(IRangesList(a=range1, b=range2, compress=compress)))
  }
}

test_IRangesList_as_data_frame <- function() {
  for (compress in c(TRUE, FALSE)) {
    range1 <- IRanges(start=c(1,2,3), end=c(5,2,8))
    range2 <- IRanges(start=c(15,45,20,1), end=c(15,100,80,5))
    rl <- IRangesList(range1, range2, compress=compress)
    df <- data.frame(group=togroup(PartitioningByWidth(rl)),
                     group_name=NA_character_,
                     as.data.frame(c(range1,range2)), stringsAsFactors=FALSE)
    checkIdentical(df, as.data.frame(rl))
    names(rl) <- c("a", "b")
    df$group_name <- c("a", "b")[togroup(PartitioningByWidth(rl))]
    checkIdentical(df, as.data.frame(rl))
  }
}

test_IRangesList_annotation <- function() {
  range1 <- IRanges(start=c(1,2,3), end=c(5,2,8))
  range2 <- IRanges(start=c(15,45,20,1), end=c(15,100,80,5))
  for (compress in c(TRUE, FALSE)) {
    rl <- IRangesList(range1, range2, compress = compress)
    mcols(rl) <- DataFrame(a = 1:2)
    checkIdentical(mcols(rl)[,1], 1:2)
    checkIdentical(mcols(rl[2:1])[,1], 2:1)
    checkIdentical(mcols(c(rl,rl))[,1], rep(1:2,2))
    checkIdentical(mcols(append(rl,rl))[,1], rep(1:2,2))
  }
}

## test_IRangesList_overlap <- function() {
##   rl1 <- IRangesList(a = IRanges(c(1,2),c(4,3)), b = IRanges(c(4,6),c(10,7)))
##   rl2 <- IRangesList(b = IRanges(c(0,2),c(4,5)), a = IRanges(c(4,5),c(6,7)))
##   overlap(rl1, rl2)
##   overlap(rl1, rl2, select = "first")
##   overlap(rl1, rl2, select = "first", drop = TRUE)
##   names(rl2)[1] <- "c"
##   overlap(rl1, rl2)
##   overlap(rl1, rl2, select = "first")
##   overlap(rl1, rl2, select = "first", drop = TRUE)
##   names(rl2) <- NULL
##   overlap(rl1, rl2)
##   overlap(rl1, rl2, select = "first")
##   overlap(rl1, rl2, select = "first", drop = TRUE)
##   overlap(rl1, rl2[1])
##   overlap(rl1, rl2[1], select = "first")
##   overlap(rl1, rl2[1], select = "first", drop = TRUE)
##   overlap(rl1[1], rl2)
##   overlap(rl1[1], rl2, select = "first")
##   overlap(rl1[1], rl2, select = "first", drop = TRUE)
## }