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Viewing changes to inst/unitTests/test_findOverlaps-methods.R

  • Committer: Package Import Robot
  • Author(s): Andreas Tille
  • Date: 2014-06-13 15:04:19 UTC
  • mfrom: (1.1.2)
  • Revision ID: package-import@ubuntu.com-20140613150419-v49mxnlg42rnuks5
Tags: 1.16.3-1
* New upstream version
* New (Build-)Depends: r-bioc-genomeinfodb
* cme fix dpkg-control
* add autopkgtest

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inst/unitTests/test_findOverlaps-methods.R
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                   subjectHits = unname(matchMatrix3[ , 2L]),
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                   queryLength = 4L, subjectLength = 4L)
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    checkIdentical(target3, current3)
 
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    ## type = "within"
 
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    q0 <- GRanges("A", IRanges(c(11, 5, 4, 11, 11, 4), 
 
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                     c(30, 30, 30, 50, 51, 51)))
 
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    s0 <- GRanges("A", IRanges(5, width=46))
 
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    s0@seqinfo <- Seqinfo(seqnames="A", seqlengths=100, isCircular=TRUE)
 
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    ## sanity check with linear shift 
 
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    fo0 <- findOverlaps(q0, s0, type="within")
 
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    expected <- c(1L, 2L, 4L)
 
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    checkIdentical(queryHits(fo0), expected)
 
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    A=90
 
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    q1 <- shift(q0, A)
 
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    s1 <- shift(s0, A)
 
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    fo1 <- findOverlaps(q1, s1, type="within")
 
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    checkIdentical(queryHits(fo1), expected)
 
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    ## circular shift 
 
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    n1=-1; n2=0
 
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    q2 <- shift(q0, A + 100 * n1)
 
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    s2 <- shift(s0, A + 100 * n2)
 
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    fo1 <- findOverlaps(q1, s1, type="within")
 
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    checkIdentical(queryHits(fo1), expected)
 
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    ## With A of length 8 --> range 3 is within range 2 
 
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    gr <- GRanges(seqnames=rep.int("A", 4),
 
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                  ranges=IRanges(start=c(2, 4, 6, 8), width=c(3, 3, 3, 5)))
 
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    gr@seqinfo <- Seqinfo(seqnames="A", seqlengths=8, isCircular=TRUE)
 
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    current4 <- findOverlaps(gr, gr, type="within")
 
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    matchMatrix4 <- matrix(c(1L, 1L, 2L, 3L, 4L, 
 
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                             1L, 4L, 2L, 3L, 4L), ncol = 2,
 
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                           dimnames = list(NULL, c("queryHits", "subjectHits")))
 
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    target4 <- new("Hits",
 
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                   queryHits = unname(matchMatrix4[ , 1L]),
 
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                   subjectHits = unname(matchMatrix4[ , 2L]),
 
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                   queryLength = 4L, subjectLength = 4L)
 
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    checkIdentical(target4, current4)
 
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    ## With A of length 9 --> range 3 is not within range 2 
 
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    gr@seqinfo <- Seqinfo(seqnames="A", seqlengths=9, isCircular=TRUE)
 
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    current5 <- findOverlaps(gr, gr, type="within")
 
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    target5 <- new("Hits",
 
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                   queryHits = unname(matchMatrix2[ , 1L]),
 
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                   subjectHits = unname(matchMatrix2[ , 2L]),
 
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                   queryLength = 4L, subjectLength = 4L)
 
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    checkIdentical(target5, current5)
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}
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