tests/testthat/test-getBestAlnInfo.R
In LihuaJulieZhu/GUIDEseq: GUIDE-seq and PEtag-seq analysis pipeline
# pa.f <- readRDS(file = system.file("extdata", "pa.f.RDS",
# package = "GUIDEseq"))
# pa.r <- readRDS(file = system.file("extdata", "pa.r.RDS",
# package = "GUIDEseq"))
subjects2 <- readRDS(file = system.file("extdata", "subjects2.RDS",
package = "GUIDEseq"))
# hg19
gRNA <- "TTGCTTTTATCACAGGCTCC"
pa.f<- lapply(1:length(subjects2), function(i) {
pairwiseAlignment(pattern = gRNA,
subject = as.character(subjects2[i]),
type = "global-local",
scoreOnly = FALSE)
})
pa.r <- lapply(1:length(subjects2), function(i) {
pairwiseAlignment(pattern = gRNA,
subject = as.character(reverseComplement(subjects2[i])),
type = "global-local",
scoreOnly = FALSE)
})
#saveRDS(pa.f, file = "~/Dropbox (UMass Medical School)/Bioconductor/Trunk/GUIDEseq/inst/extdata/pa.f.RDS")
#saveRDS(pa.r, file = "~/Dropbox (UMass Medical School)/Bioconductor/Trunk/GUIDEseq/inst/extdata/pa.r.RDS")
test_that("getBestAlnInfo plus strand bulge in gRNA works", {
i = 16
temp <- getBestAlnInfo(subjects2[i], pa.f[[i]], pa.r[[i]])
expect_equal(
as.character(reverseComplement(DNAString(substr(as.character(subjects2[i]),
temp$offTarget_Start, temp$offTarget_End)))),
"TTCCATTCAATGATTCCATT")
expect_equal(temp$offTargetStrand, "-")
expect_equal(temp$guideAlignment2OffTarget, "..C.A..---..AT.AT...")
expect_equal(temp$n.mismatch, 6)
expect_equal(temp$n.insertion, 3)
expect_equal(temp$n.deletion, 0)
expect_equal(temp$pos.insertion, c(8,9,10))
expect_equal(temp$pos.mismatch, c(3, 5, 13, 14, 16, 17))
})
test_that("getBestAlnInfo plus strand bulge in gRNA works", {
i = 123
temp <- getBestAlnInfo(subjects2[i], pa.f[[i]], pa.r[[i]])
expect_equal(
as.character(substr(as.character(subjects2[i]),
temp$offTarget_Start, temp$offTarget_End)),
"ATGGTTTCAAAACTGCTCCATC")
expect_equal(temp$offTarget, "chrX+:61721170:61721195chrX-:61721140:61721165")
expect_equal(as.character(temp$PAM.sequence),"ATC")
expect_equal(temp$offTarget_sequence, "ATGGTTTCAAAACTG-CTCCATC")
expect_equal(temp$offTargetStrand, "+")
expect_equal(temp$offTarget_End, 57)
expect_equal(temp$offTarget_Start, 36)
expect_equal(temp$guideAlignment2OffTarget, "A..G...C.AA..T.-....")
expect_equal(temp$n.PAM.mismatch, 2)
expect_equal(temp$mismatch.distance2PAM, "20,17,13,11,10,7")
expect_equal(as.numeric(temp$pos.insertion), 16)
expect_equal(temp$pos.mismatch, c(1, 4, 8, 10, 11, 14))
# n.mismatch = mismatches + indels
expect_equal(temp$n.mismatch, 6)
expect_equal(temp$n.deletion, 0)
expect_equal(temp$n.insertion, 1)
})
test_that("getBestAlnInfo minus strand bulge in gRNA works", {
i = 66
temp <- getBestAlnInfo(subjects2[i], pa.f[[i]], pa.r[[i]])
expect_equal(
as.character(reverseComplement(DNAString(substr(subjects2[i],
temp$offTarget_Start, temp$offTarget_End)))),
"TTGCATTATTTCAGCATCTCAT")
expect_equal(temp$offTarget,
"chr2+:221535820:221535845chr2-:221535730:221535755"
)
expect_equal(temp$offTargetStrand, "-")
expect_equal(as.character(temp$PAM.sequence),"CAT")
expect_equal(temp$offTarget_sequence, "TTGCATT-ATTTCAGCATCTCAT")
expect_equal(temp$offTarget_End, 71)
expect_equal(temp$offTarget_Start, 50)
expect_equal(temp$guideAlignment2OffTarget, "....A..-..TT...CA..T")
expect_equal(temp$n.PAM.mismatch, 2)
expect_equal(temp$mismatch.distance2PAM, "16,10,9,5,4,1") ###
expect_equal(as.numeric(temp$pos.insertion), 8)
expect_equal(temp$pos.mismatch, c(5,11,12,16,17,20))
# n.mismatch = mismatches + indels
expect_equal(temp$n.mismatch, 6)
expect_equal(temp$pos.insertion, 8)
expect_equal(temp$n.insertion, 1)
})
test_that("getBestAlnInfo plus strand without indel works", {
i = 1
#pattern: TTGCTTTTATCACAGGCTCC
#subject: [84] GTGTGTTTGGAAACTGCTCC
temp <- getBestAlnInfo(subjects2[i], pa.f[[i]], pa.r[[i]])
expected_mismatch_pos <- c(1, 4,5, 9, 10, 11, 13, 14, 15)
expect_equal(temp$pos.mismatch, expected_mismatch_pos)
expect_equal(temp$offTarget_End, 106)
expect_equal(temp$offTarget_Start, 84)
expect_equal(
as.character(substr(as.character(subjects2[i]),
temp$offTarget_Start, temp$offTarget_End)),
temp$offTarget_sequence)
expect_equal(temp$offTarget,names(subjects2[i]))
expect_equal(temp$offTargetStrand, "+")
expect_equal(as.character(temp$PAM.sequence),"ATC")
expect_equal(temp$guideAlignment2OffTarget, "G..TG...GGA.ACT.....")
expect_equal(temp$n.PAM.mismatch, 2)
expect_equal(temp$mismatch.distance2PAM, "20,17,16,12,11,10,8,7,6")
# n.mismatch = mismatches + indels
expect_equal(temp$n.mismatch, 9)
expect_equal(temp$n.insertion, 0)
expect_equal(temp$n.deletion, 0)
})
test_that("getBestAlnInfo minus strand with deletion on gRNA works", {
i = 96
#pattern: GGAGCCTGTGATAAAAGCAA
#subject: [48] GAAGCCTATGCTAGAAATGG
temp <- getBestAlnInfo(subjects2[i], pa.f[[i]], pa.r[[i]])
expect_equal(temp$offTarget_End, 69)
expect_equal(temp$offTarget_Start, 45)
expect_equal(
as.character(substr(as.character(subjects2[i]),
temp$offTarget_Start, temp$offTarget_End)),
as.character(reverseComplement(DNAString(temp$offTarget_sequence))))
expect_equal(temp$offTarget,names(subjects2[i]))
expect_equal(temp$offTargetStrand, "-")
expect_equal(as.character(reverseComplement(DNAString(
as.character(temp$PAM.sequence)))),
as.character(substr(as.character(subjects2[i]),
temp$offTarget_Start, temp$offTarget_Start + 2)))
expect_equal(temp$guideAlignment2OffTarget, "..C.A..^^..G..T.....T.")
expect_equal(temp$mismatch.distance2PAM, "18,16,11,8,2")
expect_equal(temp$pos.mismatch, c(3,5, 10, 13, 19))
expect_equal(temp$n.PAM.mismatch, 1)
# n.mismatch = mismatches + indels
expect_equal(temp$n.mismatch, 5)
expect_equal(temp$n.deletion, 2)
expect_equal(temp$n.insertion, 0)
})
#Global-Local PairwiseAlignmentsSingleSubject (1 of 1)
#pattern: TGCTTGGTCGG-CACTGATAG
#subject: [15] GGCTTGGCCGGGCACTGATTG
test_that("getBestAlnInfo plus strand with bulge in offtargets works", {
chr14OT <- readRDS(file = system.file(
"extdata", "InsertionInOfftarget.RDS",
package = "GUIDEseq"))
subjects1 <- chr14OT[[3]]
gRNA <- "TGCTTGGTCGGCACTGATAG"
pa.f<- lapply(1:length(subjects1), function(i) {
pairwiseAlignment(pattern = gRNA,
subject = as.character(subjects1[i]),
type = "global-local",
scoreOnly = FALSE)
})
pa.r <- lapply(1:length(subjects1), function(i) {
pairwiseAlignment(pattern = gRNA,
subject = as.character(reverseComplement(subjects1[i])),
type = "global-local",
scoreOnly = FALSE)
})
i <- 1
temp <- getBestAlnInfo(subjects1[i], pa.f[[i]], pa.r[[i]])
expect_equal(as.numeric(temp$pos.deletion), 10)
expect_equal(temp$pos.mismatch, c(1,8,19))
expect_equal(temp$offTarget_End, 38)
expect_equal(temp$offTarget_Start, 15)
expect_equal(
as.character(substr(as.character(subjects1[i]),
temp$offTarget_Start, temp$offTarget_End)),
temp$offTarget_sequence)
expect_equal(temp$offTarget,names(subjects1[i]))
expect_equal(temp$offTargetStrand, "+")
PAM.size <- 3
expect_equal(
as.character(temp$PAM.sequence),
as.character(substr(as.character(subjects1[i]),
temp$offTarget_End - PAM.size + 1, temp$offTarget_End)))
expect_equal(temp$pos.deletion, 10)
expect_equal(temp$pos.mismatch, c(1,8,19))
expect_equal(temp$guideAlignment2OffTarget, "G......C.^.........T.")
expect_equal(temp$mismatch.distance2PAM, "20,13,2")
expect_equal(temp$n.PAM.mismatch, 0)
# n.mismatch = mismatches + indels
expect_equal(temp$n.mismatch, 3)
expect_equal(temp$n.insertion, 0)
expect_equal(temp$n.deletion, 1)
})
test_that("getBestAlnInfo minus strand with perfect match in offtargets works", {
chr14OT <- readRDS(file = system.file(
"extdata", "InsertionInOfftarget.RDS",
package = "GUIDEseq"))
subjects1 <- chr14OT[[3]]
gRNA <- "TGCTTGGTCGGCACTGATAG"
pa.f<- lapply(1:length(subjects1), function(i) {
pairwiseAlignment(pattern = gRNA,
subject = as.character(subjects1[i]),
type = "global-local",
scoreOnly = FALSE)
})
pa.r <- lapply(1:length(subjects1), function(i) {
pairwiseAlignment(pattern = gRNA,
subject = as.character(reverseComplement(subjects1[i])),
type = "global-local",
scoreOnly = FALSE)
})
#saveRDS(list(pa.f = pa.f, pa.r = pa.r, subjects = subjects1), file =
# "~/Dropbox (UMass Medical School)/Bioconductor/Trunk/GUIDEseq/inst/extdata/InsertionInOfftarget.RDS")
#pa.f <- chr14OT[[1]]
#pa.r <- chr14OT[[2]]
i <- 2
temp <- getBestAlnInfo(subjects1[i], pa.f[[i]], pa.r[[i]])
expect_equal(temp$offTarget_End, 47)
expect_equal(temp$offTarget_Start, 25)
expect_equal(
as.character(substr(as.character(subjects1[i]),
temp$offTarget_Start, temp$offTarget_End)),
as.character(reverseComplement(DNAString(temp$offTarget_sequence))))
expect_equal(temp$offTarget,names(subjects1[i]))
expect_equal(temp$offTargetStrand, "-")
expect_equal(as.character(reverseComplement(DNAString(
as.character(temp$PAM.sequence)))),
as.character(substr(as.character(subjects1[i]),
temp$offTarget_Start, temp$offTarget_Start + 2)))
expect_equal(temp$guideAlignment2OffTarget, paste0(rep(".", 20),
collapse = ""))
expect_equal(temp$mismatch.distance2PAM, "")
expect_equal(temp$n.PAM.mismatch, 0)
# n.mismatch = mismatches + indels
expect_equal(temp$n.mismatch, 0)
expect_equal(temp$n.insertion, 0)
expect_equal(temp$n.deletion, 0)
})
test_that("getBestAlnInfo plus strand with bulge in both guide (first) and OT works", {
gRNA <- "CTTGCCCCACAGGGCAGTAA"
peak <- "CTAGCTCTCACAGGAACTAA"
pa.f<- pairwiseAlignment(pattern = gRNA,
subject = peak,
type = "global-local",
scoreOnly = FALSE)
pa.r <- pairwiseAlignment(pattern = gRNA,
subject = as.character(reverseComplement(DNAString(peak))),
type = "global-local",
scoreOnly = FALSE)
temp <- getBestAlnInfo(peak, pa.f, pa.r)
expect_equal(temp$offTarget_sequence, "CTAGCTCTCACAGGA-ACTAA")
expect_equal(temp$guideAlignment2OffTarget , "..A..T.^......A-.C...")
expect_equal(temp$offTargetStrand, "+")
expect_equal(temp$pos.mismatch, c(3, 6, 14, 17))
expect_equal(temp$n.insertion, 1)
expect_equal(temp$n.deletion, 1)
expect_equal(temp$pos.insertion, 15)
expect_equal(temp$pos.deletion, 8)
})
test_that("getBestAlnInfo plus strand with bulge in both guide (second) and OT (first) works", {
peak <- "CTTGCCCCACAGGGCAGTAA"
gRNA <- "CTAGCTCTCACAGGAACTAA"
pa.f<- pairwiseAlignment(pattern = gRNA,
subject = peak,
type = "global-local",
scoreOnly = FALSE)
pa.r <- pairwiseAlignment(pattern = gRNA,
subject = as.character(reverseComplement(DNAString(peak))),
type = "global-local",
scoreOnly = FALSE)
temp <- getBestAlnInfo(peak, pa.f, pa.r)
expect_equal(temp$offTarget_sequence, "CTTGCCC-CACAGGGCAGTAA")
expect_equal(temp$offTargetStrand, "+")
expect_equal(temp$pos.mismatch, c(3, 6, 15, 17))
expect_equal(temp$guideAlignment2OffTarget, "..T..C.-......G^.G...")
expect_equal(temp$n.insertion, 1)
expect_equal(temp$n.deletion, 1)
expect_equal(temp$pos.insertion, 8)
expect_equal(temp$pos.deletion, 16)
})
test_that("getBestAlnInfo plus strand with bulge in both guide (second) and OT (first) works", {
gRNA <- "CTTGCCCCACAGGGCAGTAA"
peak <- "ATTGCCCAGGCTTAGTGCAGTAGCGC"
pa.f<- pairwiseAlignment(pattern = gRNA,
subject = peak,
type = "global-local",
scoreOnly = FALSE)
pa.r <- pairwiseAlignment(pattern = gRNA,
subject = as.character(reverseComplement(DNAString(peak))),
type = "global-local",
scoreOnly = FALSE)
temp <- getBestAlnInfo(peak, pa.f, pa.r)
expect_equal(temp$offTarget_sequence, peak)
expect_equal(temp$offTargetStrand, "+")
expect_equal(temp$pos.mismatch, c(1, 9, 10, 13, 20))
expect_equal( temp$guideAlignment2OffTarget, "A......^^^.TT..T......G")
expect_equal(temp$n.insertion, 0)
expect_equal(temp$n.deletion, 3)
expect_equal(temp$pos.deletion, c(8,9,10))
})
LihuaJulieZhu/GUIDEseq documentation built on March 27, 2024, 9:42 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
# pa.f <- readRDS(file = system.file("extdata", "pa.f.RDS",
# package = "GUIDEseq"))
# pa.r <- readRDS(file = system.file("extdata", "pa.r.RDS",
# package = "GUIDEseq"))
subjects2 <- readRDS(file = system.file("extdata", "subjects2.RDS",
package = "GUIDEseq"))
# hg19
gRNA <- "TTGCTTTTATCACAGGCTCC"
pa.f<- lapply(1:length(subjects2), function(i) {
pairwiseAlignment(pattern = gRNA,
subject = as.character(subjects2[i]),
type = "global-local",
scoreOnly = FALSE)
})
pa.r <- lapply(1:length(subjects2), function(i) {
pairwiseAlignment(pattern = gRNA,
subject = as.character(reverseComplement(subjects2[i])),
type = "global-local",
scoreOnly = FALSE)
})
#saveRDS(pa.f, file = "~/Dropbox (UMass Medical School)/Bioconductor/Trunk/GUIDEseq/inst/extdata/pa.f.RDS")
#saveRDS(pa.r, file = "~/Dropbox (UMass Medical School)/Bioconductor/Trunk/GUIDEseq/inst/extdata/pa.r.RDS")
test_that("getBestAlnInfo plus strand bulge in gRNA works", {
i = 16
temp <- getBestAlnInfo(subjects2[i], pa.f[[i]], pa.r[[i]])
expect_equal(
as.character(reverseComplement(DNAString(substr(as.character(subjects2[i]),
temp$offTarget_Start, temp$offTarget_End)))),
"TTCCATTCAATGATTCCATT")
expect_equal(temp$offTargetStrand, "-")
expect_equal(temp$guideAlignment2OffTarget, "..C.A..---..AT.AT...")
expect_equal(temp$n.mismatch, 6)
expect_equal(temp$n.insertion, 3)
expect_equal(temp$n.deletion, 0)
expect_equal(temp$pos.insertion, c(8,9,10))
expect_equal(temp$pos.mismatch, c(3, 5, 13, 14, 16, 17))
})
test_that("getBestAlnInfo plus strand bulge in gRNA works", {
i = 123
temp <- getBestAlnInfo(subjects2[i], pa.f[[i]], pa.r[[i]])
expect_equal(
as.character(substr(as.character(subjects2[i]),
temp$offTarget_Start, temp$offTarget_End)),
"ATGGTTTCAAAACTGCTCCATC")
expect_equal(temp$offTarget, "chrX+:61721170:61721195chrX-:61721140:61721165")
expect_equal(as.character(temp$PAM.sequence),"ATC")
expect_equal(temp$offTarget_sequence, "ATGGTTTCAAAACTG-CTCCATC")
expect_equal(temp$offTargetStrand, "+")
expect_equal(temp$offTarget_End, 57)
expect_equal(temp$offTarget_Start, 36)
expect_equal(temp$guideAlignment2OffTarget, "A..G...C.AA..T.-....")
expect_equal(temp$n.PAM.mismatch, 2)
expect_equal(temp$mismatch.distance2PAM, "20,17,13,11,10,7")
expect_equal(as.numeric(temp$pos.insertion), 16)
expect_equal(temp$pos.mismatch, c(1, 4, 8, 10, 11, 14))
# n.mismatch = mismatches + indels
expect_equal(temp$n.mismatch, 6)
expect_equal(temp$n.deletion, 0)
expect_equal(temp$n.insertion, 1)
})
test_that("getBestAlnInfo minus strand bulge in gRNA works", {
i = 66
temp <- getBestAlnInfo(subjects2[i], pa.f[[i]], pa.r[[i]])
expect_equal(
as.character(reverseComplement(DNAString(substr(subjects2[i],
temp$offTarget_Start, temp$offTarget_End)))),
"TTGCATTATTTCAGCATCTCAT")
expect_equal(temp$offTarget,
"chr2+:221535820:221535845chr2-:221535730:221535755"
)
expect_equal(temp$offTargetStrand, "-")
expect_equal(as.character(temp$PAM.sequence),"CAT")
expect_equal(temp$offTarget_sequence, "TTGCATT-ATTTCAGCATCTCAT")
expect_equal(temp$offTarget_End, 71)
expect_equal(temp$offTarget_Start, 50)
expect_equal(temp$guideAlignment2OffTarget, "....A..-..TT...CA..T")
expect_equal(temp$n.PAM.mismatch, 2)
expect_equal(temp$mismatch.distance2PAM, "16,10,9,5,4,1") ###
expect_equal(as.numeric(temp$pos.insertion), 8)
expect_equal(temp$pos.mismatch, c(5,11,12,16,17,20))
# n.mismatch = mismatches + indels
expect_equal(temp$n.mismatch, 6)
expect_equal(temp$pos.insertion, 8)
expect_equal(temp$n.insertion, 1)
})
test_that("getBestAlnInfo plus strand without indel works", {
i = 1
#pattern: TTGCTTTTATCACAGGCTCC
#subject: [84] GTGTGTTTGGAAACTGCTCC
temp <- getBestAlnInfo(subjects2[i], pa.f[[i]], pa.r[[i]])
expected_mismatch_pos <- c(1, 4,5, 9, 10, 11, 13, 14, 15)
expect_equal(temp$pos.mismatch, expected_mismatch_pos)
expect_equal(temp$offTarget_End, 106)
expect_equal(temp$offTarget_Start, 84)
expect_equal(
as.character(substr(as.character(subjects2[i]),
temp$offTarget_Start, temp$offTarget_End)),
temp$offTarget_sequence)
expect_equal(temp$offTarget,names(subjects2[i]))
expect_equal(temp$offTargetStrand, "+")
expect_equal(as.character(temp$PAM.sequence),"ATC")
expect_equal(temp$guideAlignment2OffTarget, "G..TG...GGA.ACT.....")
expect_equal(temp$n.PAM.mismatch, 2)
expect_equal(temp$mismatch.distance2PAM, "20,17,16,12,11,10,8,7,6")
# n.mismatch = mismatches + indels
expect_equal(temp$n.mismatch, 9)
expect_equal(temp$n.insertion, 0)
expect_equal(temp$n.deletion, 0)
})
test_that("getBestAlnInfo minus strand with deletion on gRNA works", {
i = 96
#pattern: GGAGCCTGTGATAAAAGCAA
#subject: [48] GAAGCCTATGCTAGAAATGG
temp <- getBestAlnInfo(subjects2[i], pa.f[[i]], pa.r[[i]])
expect_equal(temp$offTarget_End, 69)
expect_equal(temp$offTarget_Start, 45)
expect_equal(
as.character(substr(as.character(subjects2[i]),
temp$offTarget_Start, temp$offTarget_End)),
as.character(reverseComplement(DNAString(temp$offTarget_sequence))))
expect_equal(temp$offTarget,names(subjects2[i]))
expect_equal(temp$offTargetStrand, "-")
expect_equal(as.character(reverseComplement(DNAString(
as.character(temp$PAM.sequence)))),
as.character(substr(as.character(subjects2[i]),
temp$offTarget_Start, temp$offTarget_Start + 2)))
expect_equal(temp$guideAlignment2OffTarget, "..C.A..^^..G..T.....T.")
expect_equal(temp$mismatch.distance2PAM, "18,16,11,8,2")
expect_equal(temp$pos.mismatch, c(3,5, 10, 13, 19))
expect_equal(temp$n.PAM.mismatch, 1)
# n.mismatch = mismatches + indels
expect_equal(temp$n.mismatch, 5)
expect_equal(temp$n.deletion, 2)
expect_equal(temp$n.insertion, 0)
})
#Global-Local PairwiseAlignmentsSingleSubject (1 of 1)
#pattern: TGCTTGGTCGG-CACTGATAG
#subject: [15] GGCTTGGCCGGGCACTGATTG
test_that("getBestAlnInfo plus strand with bulge in offtargets works", {
chr14OT <- readRDS(file = system.file(
"extdata", "InsertionInOfftarget.RDS",
package = "GUIDEseq"))
subjects1 <- chr14OT[[3]]
gRNA <- "TGCTTGGTCGGCACTGATAG"
pa.f<- lapply(1:length(subjects1), function(i) {
pairwiseAlignment(pattern = gRNA,
subject = as.character(subjects1[i]),
type = "global-local",
scoreOnly = FALSE)
})
pa.r <- lapply(1:length(subjects1), function(i) {
pairwiseAlignment(pattern = gRNA,
subject = as.character(reverseComplement(subjects1[i])),
type = "global-local",
scoreOnly = FALSE)
})
i <- 1
temp <- getBestAlnInfo(subjects1[i], pa.f[[i]], pa.r[[i]])
expect_equal(as.numeric(temp$pos.deletion), 10)
expect_equal(temp$pos.mismatch, c(1,8,19))
expect_equal(temp$offTarget_End, 38)
expect_equal(temp$offTarget_Start, 15)
expect_equal(
as.character(substr(as.character(subjects1[i]),
temp$offTarget_Start, temp$offTarget_End)),
temp$offTarget_sequence)
expect_equal(temp$offTarget,names(subjects1[i]))
expect_equal(temp$offTargetStrand, "+")
PAM.size <- 3
expect_equal(
as.character(temp$PAM.sequence),
as.character(substr(as.character(subjects1[i]),
temp$offTarget_End - PAM.size + 1, temp$offTarget_End)))
expect_equal(temp$pos.deletion, 10)
expect_equal(temp$pos.mismatch, c(1,8,19))
expect_equal(temp$guideAlignment2OffTarget, "G......C.^.........T.")
expect_equal(temp$mismatch.distance2PAM, "20,13,2")
expect_equal(temp$n.PAM.mismatch, 0)
# n.mismatch = mismatches + indels
expect_equal(temp$n.mismatch, 3)
expect_equal(temp$n.insertion, 0)
expect_equal(temp$n.deletion, 1)
})
test_that("getBestAlnInfo minus strand with perfect match in offtargets works", {
chr14OT <- readRDS(file = system.file(
"extdata", "InsertionInOfftarget.RDS",
package = "GUIDEseq"))
subjects1 <- chr14OT[[3]]
gRNA <- "TGCTTGGTCGGCACTGATAG"
pa.f<- lapply(1:length(subjects1), function(i) {
pairwiseAlignment(pattern = gRNA,
subject = as.character(subjects1[i]),
type = "global-local",
scoreOnly = FALSE)
})
pa.r <- lapply(1:length(subjects1), function(i) {
pairwiseAlignment(pattern = gRNA,
subject = as.character(reverseComplement(subjects1[i])),
type = "global-local",
scoreOnly = FALSE)
})
#saveRDS(list(pa.f = pa.f, pa.r = pa.r, subjects = subjects1), file =
# "~/Dropbox (UMass Medical School)/Bioconductor/Trunk/GUIDEseq/inst/extdata/InsertionInOfftarget.RDS")
#pa.f <- chr14OT[[1]]
#pa.r <- chr14OT[[2]]
i <- 2
temp <- getBestAlnInfo(subjects1[i], pa.f[[i]], pa.r[[i]])
expect_equal(temp$offTarget_End, 47)
expect_equal(temp$offTarget_Start, 25)
expect_equal(
as.character(substr(as.character(subjects1[i]),
temp$offTarget_Start, temp$offTarget_End)),
as.character(reverseComplement(DNAString(temp$offTarget_sequence))))
expect_equal(temp$offTarget,names(subjects1[i]))
expect_equal(temp$offTargetStrand, "-")
expect_equal(as.character(reverseComplement(DNAString(
as.character(temp$PAM.sequence)))),
as.character(substr(as.character(subjects1[i]),
temp$offTarget_Start, temp$offTarget_Start + 2)))
expect_equal(temp$guideAlignment2OffTarget, paste0(rep(".", 20),
collapse = ""))
expect_equal(temp$mismatch.distance2PAM, "")
expect_equal(temp$n.PAM.mismatch, 0)
# n.mismatch = mismatches + indels
expect_equal(temp$n.mismatch, 0)
expect_equal(temp$n.insertion, 0)
expect_equal(temp$n.deletion, 0)
})
test_that("getBestAlnInfo plus strand with bulge in both guide (first) and OT works", {
gRNA <- "CTTGCCCCACAGGGCAGTAA"
peak <- "CTAGCTCTCACAGGAACTAA"
pa.f<- pairwiseAlignment(pattern = gRNA,
subject = peak,
type = "global-local",
scoreOnly = FALSE)
pa.r <- pairwiseAlignment(pattern = gRNA,
subject = as.character(reverseComplement(DNAString(peak))),
type = "global-local",
scoreOnly = FALSE)
temp <- getBestAlnInfo(peak, pa.f, pa.r)
expect_equal(temp$offTarget_sequence, "CTAGCTCTCACAGGA-ACTAA")
expect_equal(temp$guideAlignment2OffTarget , "..A..T.^......A-.C...")
expect_equal(temp$offTargetStrand, "+")
expect_equal(temp$pos.mismatch, c(3, 6, 14, 17))
expect_equal(temp$n.insertion, 1)
expect_equal(temp$n.deletion, 1)
expect_equal(temp$pos.insertion, 15)
expect_equal(temp$pos.deletion, 8)
})
test_that("getBestAlnInfo plus strand with bulge in both guide (second) and OT (first) works", {
peak <- "CTTGCCCCACAGGGCAGTAA"
gRNA <- "CTAGCTCTCACAGGAACTAA"
pa.f<- pairwiseAlignment(pattern = gRNA,
subject = peak,
type = "global-local",
scoreOnly = FALSE)
pa.r <- pairwiseAlignment(pattern = gRNA,
subject = as.character(reverseComplement(DNAString(peak))),
type = "global-local",
scoreOnly = FALSE)
temp <- getBestAlnInfo(peak, pa.f, pa.r)
expect_equal(temp$offTarget_sequence, "CTTGCCC-CACAGGGCAGTAA")
expect_equal(temp$offTargetStrand, "+")
expect_equal(temp$pos.mismatch, c(3, 6, 15, 17))
expect_equal(temp$guideAlignment2OffTarget, "..T..C.-......G^.G...")
expect_equal(temp$n.insertion, 1)
expect_equal(temp$n.deletion, 1)
expect_equal(temp$pos.insertion, 8)
expect_equal(temp$pos.deletion, 16)
})
test_that("getBestAlnInfo plus strand with bulge in both guide (second) and OT (first) works", {
gRNA <- "CTTGCCCCACAGGGCAGTAA"
peak <- "ATTGCCCAGGCTTAGTGCAGTAGCGC"
pa.f<- pairwiseAlignment(pattern = gRNA,
subject = peak,
type = "global-local",
scoreOnly = FALSE)
pa.r <- pairwiseAlignment(pattern = gRNA,
subject = as.character(reverseComplement(DNAString(peak))),
type = "global-local",
scoreOnly = FALSE)
temp <- getBestAlnInfo(peak, pa.f, pa.r)
expect_equal(temp$offTarget_sequence, peak)
expect_equal(temp$offTargetStrand, "+")
expect_equal(temp$pos.mismatch, c(1, 9, 10, 13, 20))
expect_equal( temp$guideAlignment2OffTarget, "A......^^^.TT..T......G")
expect_equal(temp$n.insertion, 0)
expect_equal(temp$n.deletion, 3)
expect_equal(temp$pos.deletion, c(8,9,10))
})
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.