tests/testthat/test_linkMultipleVariants.R
In fmicompbio/mutscan: Preprocessing and Analysis of Deep Mutational Scanning Data
test_that("linkMultipleVariants works", {
## Fails with the wrong input
## ------------------------------------------------------------------------
expect_error(linkMultipleVariants(combinedDigestParams = 1),
"'combinedDigestParams' must be of class 'list'")
expect_error(linkMultipleVariants(combinedDigestParams = list(1)),
"'namescombinedDigestParams' must not be NULL")
expect_error(linkMultipleVariants(combinedDigestParams = list(unknown = 1)),
"All values in 'namescombinedDigestParams' must be one of")
expect_error(linkMultipleVariants(combinedDigestParams = list(fastqForward = 1),
secondArg = 1),
"'parms' must be of class 'list'")
expect_error(linkMultipleVariants(combinedDigestParams = list(fastqForward = 1),
secondArg = list(1)),
"'namesparms' must not be NULL")
expect_error(linkMultipleVariants(combinedDigestParams = list(fastqForward = 1),
secondArg = list(unknown = 1)),
"All values in 'namesparms' must be one of")
expect_error(linkMultipleVariants(combinedDigestParams = list(fastqForward = 1),
secondArg = list(elementsForward = "CC")),
"Each separate run must contain at least one variable")
expect_error(linkMultipleVariants(combinedDigestParams = list(fastqForward = 1),
secondArg = list(elementsForward = "V",
elementsReverse = "V")),
"A separate run can not have variable sequences in both")
expect_error(linkMultipleVariants(combinedDigestParams = list(fastqForward = 1),
secondArg = list(elementsForward = "VV")),
"A separate run can have at most one variable segment")
## Works with correct input
## ------------------------------------------------------------------------
## Read truth
truth <- readRDS(system.file("extdata", "multipleVariableRegions_truth.rds",
package = "mutscan"))
verbose <- FALSE
## ------------------------------------------------------------------------
## Don't filter by mutations in constant sequence
res <- linkMultipleVariants(
combinedDigestParams = list(
fastqForward = system.file("extdata", "multipleVariableRegions_R1.fastq.gz",
package = "mutscan"),
fastqReverse = system.file("extdata", "multipleVariableRegions_R2.fastq.gz",
package = "mutscan"),
elementsForward = "CVCVCV", elementLengthsForward = c(6, 24, 10, 30, 10, -1),
elementsReverse = "CVCV", elementLengthsReverse = c(6, 40, 10, -1),
mergeForwardReverse = TRUE, minOverlap = 20,
maxOverlap = 30, maxFracMismatchOverlap = 0,
revComplForward = FALSE, revComplReverse = TRUE,
avePhredMinForward = 20, avePhredMinReverse = 20,
verbose = verbose),
barcode = list(
fastqForward = system.file("extdata", "multipleVariableRegions_R1.fastq.gz",
package = "mutscan"),
elementsForward = "CVCSCS", elementLengthsForward = c(6, 24, 10, 30, 10, -1),
avePhredMinForward = 20,
collapseMaxDist = 1, collapseMinScore = 1, collapseMinRatio = 1,
verbose = verbose),
V2 = list(
fastqForward = system.file("extdata", "multipleVariableRegions_R1.fastq.gz",
package = "mutscan"),
fastqReverse = system.file("extdata", "multipleVariableRegions_R2.fastq.gz",
package = "mutscan"),
elementsForward = "CSCVCS", elementLengthsForward = c(6, 24, 10, 30, 10, -1),
elementsReverse = "CSCV", elementLengthsReverse = c(6, 40, 10, -1),
mergeForwardReverse = TRUE, minOverlap = 10,
maxOverlap = 20, maxFracMismatchOverlap = 0,
revComplForward = FALSE, revComplReverse = TRUE,
avePhredMinForward = 20, avePhredMinReverse = 20,
wildTypeForward = truth$WTV2,
nbrMutatedCodonsMaxForward = -1, nbrMutatedBasesMaxForward = 1,
forbiddenMutatedCodonsForward = "", collapseToWTForward = FALSE,
verbose = verbose, useTreeWTmatch = TRUE),
V3 = list(
fastqForward = system.file("extdata", "multipleVariableRegions_R1.fastq.gz",
package = "mutscan"),
fastqReverse = system.file("extdata", "multipleVariableRegions_R2.fastq.gz",
package = "mutscan"),
elementsForward = "CSCSCV", elementLengthsForward = c(6, 24, 10, 30, 10, -1),
elementsReverse = "CVCS", elementLengthsReverse = c(6, 40, 10, -1),
mergeForwardReverse = TRUE, minOverlap = 5,
maxOverlap = 15, maxFracMismatchOverlap = 0,
revComplForward = FALSE, revComplReverse = TRUE,
avePhredMinForward = 20, avePhredMinReverse = 20,
wildTypeForward = truth$WTV3,
nbrMutatedCodonsMaxForward = -1, nbrMutatedBasesMaxForward = 1,
forbiddenMutatedCodonsForward = "", collapseToWTForward = FALSE,
verbose = verbose, useTreeWTmatch = TRUE)
)
## Filter out only reads with N/deletions in the variable sequence
keep <- !grepl("N|del", truth$truth$status)
## Truth
correct <- truth$truth[keep, ] %>%
dplyr::group_by(trueBarcode, trueV2, trueV3) %>% dplyr::tally() %>%
dplyr::arrange(dplyr::desc(n), trueBarcode, trueV2, trueV3)
## Obs
obs <- res$countAggregated %>% dplyr::arrange(desc(nbrReads), barcode, V2, V3)
expect_equal(sum(obs$nbrReads), sum(keep))
expect_equal(correct$trueBarcode, obs$barcode)
expect_equal(correct$trueV2, obs$V2)
expect_equal(correct$trueV3, obs$V3)
expect_equal(correct$n, obs$nbrReads)
expect_equal(res$outCombined$filterSummary[, "f4_nbrNoValidOverlap"],
sum(grepl("del", truth$truth$status))) ## del
expect_equal(res$outCombined$filterSummary[, "f6_nbrTooManyNinVar"],
sum(grepl("N", truth$truth$status))) ## N
expect_equal(res$outCombined$filterSummary[, "nbrRetained"],
sum(!grepl("N|del", truth$truth$status)))
expect_equal(res$filtSeparate$barcode[, "f6_nbrTooManyNinVar"],
sum(grepl("V1N", truth$truth$status)))
expect_equal(res$filtSeparate$barcode[, "nbrRetained"],
sum(!grepl("V1N", truth$truth$status)))
expect_equal(res$filtSeparate$V2[, "f4_nbrNoValidOverlap"],
sum(grepl("del", truth$truth$status)))
expect_equal(res$filtSeparate$V2[, "nbrRetained"],
sum(!grepl("del", truth$truth$status)))
expect_equal(res$filtSeparate$V3[, "f4_nbrNoValidOverlap"],
sum(grepl("del", truth$truth$status)))
expect_equal(res$filtSeparate$V3[, "nbrRetained"],
sum(!grepl("del", truth$truth$status)))
## ------------------------------------------------------------------------
## Filter out mutations in constant sequences
res <- linkMultipleVariants(
combinedDigestParams = list(
fastqForward = system.file("extdata", "multipleVariableRegions_R1.fastq.gz",
package = "mutscan"),
fastqReverse = system.file("extdata", "multipleVariableRegions_R2.fastq.gz",
package = "mutscan"),
elementsForward = "CVCVCV", elementLengthsForward = c(6, 24, 10, 30, 10, -1),
elementsReverse = "CVCV", elementLengthsReverse = c(6, 40, 10, -1),
mergeForwardReverse = TRUE, minOverlap = 20,
maxOverlap = 30, maxFracMismatchOverlap = 0,
revComplForward = FALSE, revComplReverse = TRUE,
constantForward = truth$constFwd,
constantReverse = truth$constRev,
constantMaxDistForward = 0,
constantMaxDistReverse = 0,
avePhredMinForward = 20, avePhredMinReverse = 20,
verbose = verbose),
barcode = list(
fastqForward = system.file("extdata", "multipleVariableRegions_R1.fastq.gz",
package = "mutscan"),
elementsForward = "CVCSCS", elementLengthsForward = c(6, 24, 10, 30, 10, -1),
constantForward = truth$constFwd,
constantMaxDistForward = 0,
avePhredMinForward = 20,
collapseMaxDist = 1, collapseMinScore = 1, collapseMinRatio = 1,
verbose = verbose),
V2 = list(
fastqForward = system.file("extdata", "multipleVariableRegions_R1.fastq.gz",
package = "mutscan"),
fastqReverse = system.file("extdata", "multipleVariableRegions_R2.fastq.gz",
package = "mutscan"),
elementsForward = "CSCVCS", elementLengthsForward = c(6, 24, 10, 30, 10, -1),
elementsReverse = "CSCV", elementLengthsReverse = c(6, 40, 10, -1),
mergeForwardReverse = TRUE, minOverlap = 10,
maxOverlap = 20, maxFracMismatchOverlap = 0,
revComplForward = FALSE, revComplReverse = TRUE,
constantForward = truth$constFwd,
constantReverse = truth$constRev,
constantMaxDistForward = 0,
constantMaxDistReverse = 0,
avePhredMinForward = 20, avePhredMinReverse = 20,
wildTypeForward = truth$WTV2,
nbrMutatedCodonsMaxForward = -1, nbrMutatedBasesMaxForward = 1,
forbiddenMutatedCodonsForward = "", collapseToWTForward = FALSE,
verbose = verbose, useTreeWTmatch = TRUE),
V3 = list(
fastqForward = system.file("extdata", "multipleVariableRegions_R1.fastq.gz",
package = "mutscan"),
fastqReverse = system.file("extdata", "multipleVariableRegions_R2.fastq.gz",
package = "mutscan"),
elementsForward = "CSCSCV", elementLengthsForward = c(6, 24, 10, 30, 10, -1),
elementsReverse = "CVCS", elementLengthsReverse = c(6, 40, 10, -1),
mergeForwardReverse = TRUE, minOverlap = 5,
maxOverlap = 15, maxFracMismatchOverlap = 0,
revComplForward = FALSE, revComplReverse = TRUE,
constantForward = truth$constFwd,
constantReverse = truth$constRev,
constantMaxDistForward = 0,
constantMaxDistReverse = 0,
avePhredMinForward = 20, avePhredMinReverse = 20,
wildTypeForward = truth$WTV3,
nbrMutatedCodonsMaxForward = -1, nbrMutatedBasesMaxForward = 1,
forbiddenMutatedCodonsForward = "", collapseToWTForward = FALSE,
verbose = verbose, useTreeWTmatch = TRUE)
)
## Filter out reads with N/deletions in the variable sequence, or mutations in constant
keep <- !grepl("C.*mut|N|del", truth$truth$status)
## Truth
correct <- truth$truth[keep, ] %>%
dplyr::group_by(trueBarcode, trueV2, trueV3) %>% dplyr::tally() %>%
dplyr::arrange(dplyr::desc(n), trueBarcode, trueV2, trueV3)
## Obs
obs <- res$countAggregated %>% dplyr::arrange(desc(nbrReads), barcode, V2, V3)
expect_equal(sum(obs$nbrReads), sum(keep))
expect_equal(correct$trueBarcode, obs$barcode)
expect_equal(correct$trueV2, obs$V2)
expect_equal(correct$trueV3, obs$V3)
expect_equal(correct$n, obs$nbrReads)
## first filter out reads with deletion -> no valid overlap
## then reads with N in barcode -> too many N
## then reads with mutation in constant
expect_equal(res$outCombined$filterSummary[, "f4_nbrNoValidOverlap"],
sum(grepl("del", truth$truth$status)))
expect_equal(res$outCombined$filterSummary[, "f6_nbrTooManyNinVar"],
sum(grepl("N", truth$truth$status)))
expect_equal(res$outCombined$filterSummary[, "f12_nbrTooManyMutConstant"],
sum(grepl("C.*mut", truth$truth$status) &
!grepl("N", truth$truth$status) &
!grepl("del", truth$truth$status)))
expect_equal(res$outCombined$filterSummary[, "nbrRetained"],
sum(!grepl("C.*mut|N|del", truth$truth$status)))
expect_equal(res$filtSeparate$barcode[, "f6_nbrTooManyNinVar"],
sum(grepl("V1N", truth$truth$status)))
expect_equal(res$filtSeparate$barcode[, "f12_nbrTooManyMutConstant"],
sum(grepl("C[1-3]mut|del", truth$truth$status) &
!grepl("V1N", truth$truth$status)))
expect_equal(res$filtSeparate$barcode[, "nbrRetained"],
sum(!grepl("V1N|C[1-3]mut|del", truth$truth$status)))
expect_equal(res$filtSeparate$V2[, "f4_nbrNoValidOverlap"],
sum(grepl("del", truth$truth$status)))
expect_equal(res$filtSeparate$V2[, "f12_nbrTooManyMutConstant"],
sum(grepl("C.*mut", truth$truth$status) &
!grepl("del", truth$truth$status)))
expect_equal(res$filtSeparate$V2[, "nbrRetained"],
sum(!grepl("C.*mut|del", truth$truth$status)))
expect_equal(res$filtSeparate$V3[, "f4_nbrNoValidOverlap"],
sum(grepl("del", truth$truth$status)))
expect_equal(res$filtSeparate$V3[, "f12_nbrTooManyMutConstant"],
sum(grepl("C.*mut", truth$truth$status) &
!grepl("del", truth$truth$status)))
expect_equal(res$filtSeparate$V3[, "nbrRetained"],
sum(!grepl("C.*mut|del", truth$truth$status)))
## ------------------------------------------------------------------------
## Collapse to WT
res <- linkMultipleVariants(
combinedDigestParams = list(
fastqForward = system.file("extdata", "multipleVariableRegions_R1.fastq.gz",
package = "mutscan"),
fastqReverse = system.file("extdata", "multipleVariableRegions_R2.fastq.gz",
package = "mutscan"),
elementsForward = "CVCVCV", elementLengthsForward = c(6, 24, 10, 30, 10, -1),
elementsReverse = "CVCV", elementLengthsReverse = c(6, 40, 10, -1),
mergeForwardReverse = TRUE, minOverlap = 20,
maxOverlap = 30, maxFracMismatchOverlap = 0,
revComplForward = FALSE, revComplReverse = TRUE,
avePhredMinForward = 20, avePhredMinReverse = 20,
verbose = verbose),
barcode = list(
fastqForward = system.file("extdata", "multipleVariableRegions_R1.fastq.gz",
package = "mutscan"),
elementsForward = "CVCSCS", elementLengthsForward = c(6, 24, 10, 30, 10, -1),
avePhredMinForward = 20,
collapseMaxDist = 1, collapseMinScore = 1, collapseMinRatio = 1,
verbose = verbose),
V2 = list(
fastqForward = system.file("extdata", "multipleVariableRegions_R1.fastq.gz",
package = "mutscan"),
fastqReverse = system.file("extdata", "multipleVariableRegions_R2.fastq.gz",
package = "mutscan"),
elementsForward = "CSCVCS", elementLengthsForward = c(6, 24, 10, 30, 10, -1),
elementsReverse = "CSCV", elementLengthsReverse = c(6, 40, 10, -1),
mergeForwardReverse = TRUE, minOverlap = 10,
maxOverlap = 20, maxFracMismatchOverlap = 0,
revComplForward = FALSE, revComplReverse = TRUE,
avePhredMinForward = 20, avePhredMinReverse = 20,
wildTypeForward = truth$WTV2,
nbrMutatedCodonsMaxForward = -1, nbrMutatedBasesMaxForward = 1,
forbiddenMutatedCodonsForward = "", collapseToWTForward = TRUE,
verbose = verbose, useTreeWTmatch = TRUE),
V3 = list(
fastqForward = system.file("extdata", "multipleVariableRegions_R1.fastq.gz",
package = "mutscan"),
fastqReverse = system.file("extdata", "multipleVariableRegions_R2.fastq.gz",
package = "mutscan"),
elementsForward = "CSCSCV", elementLengthsForward = c(6, 24, 10, 30, 10, -1),
elementsReverse = "CVCS", elementLengthsReverse = c(6, 40, 10, -1),
mergeForwardReverse = TRUE, minOverlap = 5,
maxOverlap = 15, maxFracMismatchOverlap = 0,
revComplForward = FALSE, revComplReverse = TRUE,
avePhredMinForward = 20, avePhredMinReverse = 20,
wildTypeForward = truth$WTV3,
nbrMutatedCodonsMaxForward = -1, nbrMutatedBasesMaxForward = 1,
forbiddenMutatedCodonsForward = "", collapseToWTForward = TRUE,
verbose = verbose, useTreeWTmatch = TRUE)
)
## Filter out only reads with N/deletions in the variable sequence
keep <- !grepl("N|del", truth$truth$status)
## Truth
correct <- truth$truth[keep, ] %>%
dplyr::mutate(trueV2 = gsub("\\..*", "", trueV2),
trueV3 = gsub("\\..*", "", trueV3)) %>%
dplyr::group_by(trueBarcode, trueV2, trueV3) %>% dplyr::tally() %>%
dplyr::arrange(dplyr::desc(n), trueBarcode, trueV2, trueV3)
## Obs
obs <- res$countAggregated %>% dplyr::arrange(desc(nbrReads), barcode, V2, V3)
expect_equal(sum(obs$nbrReads), sum(keep))
expect_equal(correct$trueBarcode, obs$barcode)
expect_equal(correct$trueV2, obs$V2)
expect_equal(correct$trueV3, obs$V3)
expect_equal(correct$n, obs$nbrReads)
expect_equal(res$outCombined$filterSummary[, "f4_nbrNoValidOverlap"],
sum(grepl("del", truth$truth$status))) ## del
expect_equal(res$outCombined$filterSummary[, "f6_nbrTooManyNinVar"],
sum(grepl("N", truth$truth$status))) ## N
expect_equal(res$outCombined$filterSummary[, "nbrRetained"],
sum(!grepl("N|del", truth$truth$status)))
expect_equal(res$filtSeparate$barcode[, "f6_nbrTooManyNinVar"],
sum(grepl("V1N", truth$truth$status)))
expect_equal(res$filtSeparate$barcode[, "nbrRetained"],
sum(!grepl("V1N", truth$truth$status)))
expect_equal(res$filtSeparate$V2[, "f4_nbrNoValidOverlap"],
sum(grepl("del", truth$truth$status)))
expect_equal(res$filtSeparate$V2[, "nbrRetained"],
sum(!grepl("del", truth$truth$status)))
expect_equal(res$filtSeparate$V3[, "f4_nbrNoValidOverlap"],
sum(grepl("del", truth$truth$status)))
expect_equal(res$filtSeparate$V3[, "nbrRetained"],
sum(!grepl("del", truth$truth$status)))
## ------------------------------------------------------------------------
## Don't merge fwd and rev
res <- linkMultipleVariants(
combinedDigestParams = list(
fastqForward = system.file("extdata", "multipleVariableRegions_R1.fastq.gz",
package = "mutscan"),
fastqReverse = system.file("extdata", "multipleVariableRegions_R2.fastq.gz",
package = "mutscan"),
elementsForward = "CVCVCS", elementLengthsForward = c(6, 24, 10, 30, 10, -1),
elementsReverse = "CVCS", elementLengthsReverse = c(6, 40, 10, -1),
mergeForwardReverse = FALSE,
revComplForward = FALSE, revComplReverse = TRUE,
avePhredMinForward = 20, avePhredMinReverse = 20,
verbose = verbose),
barcode = list(
fastqForward = system.file("extdata", "multipleVariableRegions_R1.fastq.gz",
package = "mutscan"),
elementsForward = "CVCSCS", elementLengthsForward = c(6, 24, 10, 30, 10, -1),
avePhredMinForward = 20,
collapseMaxDist = 1, collapseMinScore = 1, collapseMinRatio = 1,
verbose = verbose),
V2 = list(
fastqForward = system.file("extdata", "multipleVariableRegions_R1.fastq.gz",
package = "mutscan"),
elementsForward = "CSCVCS", elementLengthsForward = c(6, 24, 10, 30, 10, -1),
mergeForwardReverse = FALSE,
revComplForward = FALSE, revComplReverse = TRUE,
avePhredMinForward = 20, avePhredMinReverse = 20,
wildTypeForward = truth$WTV2,
nbrMutatedCodonsMaxForward = -1, nbrMutatedBasesMaxForward = 1,
forbiddenMutatedCodonsForward = "", collapseToWTForward = FALSE,
verbose = verbose, useTreeWTmatch = TRUE),
V3 = list(
fastqForward = system.file("extdata", "multipleVariableRegions_R2.fastq.gz",
package = "mutscan"),
elementsForward = "CVCS", elementLengthsForward = c(6, 40, 10, -1),
mergeForwardReverse = FALSE,
revComplForward = TRUE,
avePhredMinForward = 20, avePhredMinReverse = 20,
wildTypeForward = truth$WTV3,
nbrMutatedCodonsMaxForward = -1, nbrMutatedBasesMaxForward = 1,
forbiddenMutatedCodonsForward = "", collapseToWTForward = FALSE,
verbose = verbose, useTreeWTmatch = TRUE)
)
## Filter out only reads with N/deletions in the variable sequence
keep <- !grepl("N|del", truth$truth$status)
## Truth
correct <- truth$truth[keep, ] %>%
dplyr::group_by(trueBarcode, trueV2, trueV3) %>% dplyr::tally() %>%
dplyr::arrange(dplyr::desc(n), trueBarcode, trueV2, trueV3)
## Obs
obs <- res$countAggregated %>% dplyr::arrange(desc(nbrReads), barcode, V2, V3)
expect_equal(sum(obs$nbrReads), sum(keep))
expect_equal(correct$trueBarcode, obs$barcode)
expect_equal(correct$trueV2, obs$V2)
expect_equal(correct$trueV3, obs$V3)
expect_equal(correct$n, obs$nbrReads)
expect_equal(res$outCombined$filterSummary[, "f6_nbrTooManyNinVar"],
sum(grepl("N", truth$truth$status)))
expect_equal(res$outCombined$filterSummary[, "nbrRetained"],
sum(!grepl("N", truth$truth$status)))
expect_equal(res$filtSeparate$barcode[, "f6_nbrTooManyNinVar"],
sum(grepl("V1N", truth$truth$status)))
expect_equal(res$filtSeparate$barcode[, "nbrRetained"],
sum(!grepl("V1N", truth$truth$status)))
expect_equal(res$filtSeparate$V2[, "f10b_nbrTooManyMutBases"],
sum(grepl("del", truth$truth$status)))
expect_equal(res$filtSeparate$V2[, "nbrRetained"],
sum(!grepl("del", truth$truth$status)))
expect_equal(res$filtSeparate$V3[, "nbrRetained"], 100)
## ------------------------------------------------------------------------
## Don't allow any mutations
res <- linkMultipleVariants(
combinedDigestParams = list(
fastqForward = system.file("extdata", "multipleVariableRegions_R1.fastq.gz",
package = "mutscan"),
fastqReverse = system.file("extdata", "multipleVariableRegions_R2.fastq.gz",
package = "mutscan"),
elementsForward = "CVCVCV", elementLengthsForward = c(6, 24, 10, 30, 10, -1),
elementsReverse = "CVCV", elementLengthsReverse = c(6, 40, 10, -1),
mergeForwardReverse = TRUE, minOverlap = 20,
maxOverlap = 30, maxFracMismatchOverlap = 0,
revComplForward = FALSE, revComplReverse = TRUE,
constantForward = truth$constFwd,
constantReverse = truth$constRev,
constantMaxDistForward = 0,
constantMaxDistReverse = 0,
avePhredMinForward = 20, avePhredMinReverse = 20,
verbose = verbose),
barcode = list(
fastqForward = system.file("extdata", "multipleVariableRegions_R1.fastq.gz",
package = "mutscan"),
elementsForward = "CVCSCS", elementLengthsForward = c(6, 24, 10, 30, 10, -1),
constantForward = truth$constFwd,
constantMaxDistForward = 0,
avePhredMinForward = 20,
collapseMaxDist = 0, collapseMinScore = 1, collapseMinRatio = 1,
verbose = verbose),
V2 = list(
fastqForward = system.file("extdata", "multipleVariableRegions_R1.fastq.gz",
package = "mutscan"),
fastqReverse = system.file("extdata", "multipleVariableRegions_R2.fastq.gz",
package = "mutscan"),
elementsForward = "CSCVCS", elementLengthsForward = c(6, 24, 10, 30, 10, -1),
elementsReverse = "CSCV", elementLengthsReverse = c(6, 40, 10, -1),
mergeForwardReverse = TRUE, minOverlap = 10,
maxOverlap = 20, maxFracMismatchOverlap = 0,
revComplForward = FALSE, revComplReverse = TRUE,
constantForward = truth$constFwd,
constantReverse = truth$constRev,
constantMaxDistForward = 0,
constantMaxDistReverse = 0,
avePhredMinForward = 20, avePhredMinReverse = 20,
wildTypeForward = truth$WTV2,
nbrMutatedCodonsMaxForward = -1, nbrMutatedBasesMaxForward = 0,
forbiddenMutatedCodonsForward = "", collapseToWTForward = FALSE,
verbose = verbose, useTreeWTmatch = TRUE),
V3 = list(
fastqForward = system.file("extdata", "multipleVariableRegions_R1.fastq.gz",
package = "mutscan"),
fastqReverse = system.file("extdata", "multipleVariableRegions_R2.fastq.gz",
package = "mutscan"),
elementsForward = "CSCSCV", elementLengthsForward = c(6, 24, 10, 30, 10, -1),
elementsReverse = "CVCS", elementLengthsReverse = c(6, 40, 10, -1),
mergeForwardReverse = TRUE, minOverlap = 5,
maxOverlap = 15, maxFracMismatchOverlap = 0,
revComplForward = FALSE, revComplReverse = TRUE,
constantForward = truth$constFwd,
constantReverse = truth$constRev,
constantMaxDistForward = 0,
constantMaxDistReverse = 0,
avePhredMinForward = 20, avePhredMinReverse = 20,
wildTypeForward = truth$WTV3,
nbrMutatedCodonsMaxForward = -1, nbrMutatedBasesMaxForward = 0,
forbiddenMutatedCodonsForward = "", collapseToWTForward = FALSE,
verbose = verbose, useTreeWTmatch = TRUE)
)
## Filter out reads with N/deletions in the variable sequence, or mutations in constant
keep <- !grepl("C.*mut|N|del|V2|V3", truth$truth$status)
## Truth
correct <- truth$truth[keep, ] %>%
dplyr::group_by(obsBarcode, trueV2, trueV3) %>% dplyr::tally() %>%
dplyr::arrange(dplyr::desc(n), obsBarcode, trueV2, trueV3)
## Obs
obs <- res$countAggregated %>% dplyr::arrange(desc(nbrReads), barcode, V2, V3)
expect_equal(sum(obs$nbrReads), sum(keep))
expect_equal(correct$obsBarcode, obs$barcode)
expect_equal(correct$trueV2, obs$V2)
expect_equal(correct$trueV3, obs$V3)
expect_equal(correct$n, obs$nbrReads)
expect_equal(res$outCombined$filterSummary[, "f4_nbrNoValidOverlap"],
sum(grepl("del", truth$truth$status)))
expect_equal(res$outCombined$filterSummary[, "f6_nbrTooManyNinVar"],
sum(grepl("N", truth$truth$status)))
expect_equal(res$outCombined$filterSummary[, "f12_nbrTooManyMutConstant"],
sum(grepl("C.*mut", truth$truth$status) &
!grepl("N", truth$truth$status) &
!grepl("del", truth$truth$status)))
expect_equal(res$outCombined$filterSummary[, "nbrRetained"],
sum(!grepl("C.*mut|N|del", truth$truth$status)))
expect_equal(res$filtSeparate$barcode[, "f6_nbrTooManyNinVar"],
sum(grepl("V1N", truth$truth$status)))
expect_equal(res$filtSeparate$barcode[, "f12_nbrTooManyMutConstant"],
sum(grepl("C[1-3]mut|del", truth$truth$status) &
!grepl("V1N", truth$truth$status)))
expect_equal(res$filtSeparate$barcode[, "nbrRetained"],
sum(!grepl("V1N|C[1-3]mut|del", truth$truth$status)))
expect_equal(res$filtSeparate$V2[, "f4_nbrNoValidOverlap"],
sum(grepl("del", truth$truth$status)))
expect_equal(res$filtSeparate$V2[, "f10b_nbrTooManyMutBases"],
sum(grepl("V2v[0-9]\\.", truth$truth$status) &
!grepl("del", truth$truth$status)))
expect_equal(res$filtSeparate$V2[, "f12_nbrTooManyMutConstant"],
sum(grepl("C.*mut", truth$truth$status) &
!grepl("del", truth$truth$status) &
!grepl("V2v[0-9]\\.", truth$truth$status)))
expect_equal(res$filtSeparate$V2[, "nbrRetained"],
sum(!grepl("C.*mut|del|V2v[0-9]\\.", truth$truth$status)))
expect_equal(res$filtSeparate$V3[, "f4_nbrNoValidOverlap"],
sum(grepl("del", truth$truth$status)))
expect_equal(res$filtSeparate$V3[, "f10b_nbrTooManyMutBases"],
sum(grepl("V3\\.", truth$truth$status) &
!grepl("del", truth$truth$status)))
expect_equal(res$filtSeparate$V3[, "f12_nbrTooManyMutConstant"],
sum(grepl("C.*mut", truth$truth$status) &
!grepl("del", truth$truth$status) &
!grepl("V3\\.", truth$truth$status)))
expect_equal(res$filtSeparate$V3[, "nbrRetained"],
sum(!grepl("C.*mut|del|V3\\.", truth$truth$status)))
})
fmicompbio/mutscan documentation built on Oct. 24, 2024, 2:41 p.m.
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test_that("linkMultipleVariants works", {
## Fails with the wrong input
## ------------------------------------------------------------------------
expect_error(linkMultipleVariants(combinedDigestParams = 1),
"'combinedDigestParams' must be of class 'list'")
expect_error(linkMultipleVariants(combinedDigestParams = list(1)),
"'namescombinedDigestParams' must not be NULL")
expect_error(linkMultipleVariants(combinedDigestParams = list(unknown = 1)),
"All values in 'namescombinedDigestParams' must be one of")
expect_error(linkMultipleVariants(combinedDigestParams = list(fastqForward = 1),
secondArg = 1),
"'parms' must be of class 'list'")
expect_error(linkMultipleVariants(combinedDigestParams = list(fastqForward = 1),
secondArg = list(1)),
"'namesparms' must not be NULL")
expect_error(linkMultipleVariants(combinedDigestParams = list(fastqForward = 1),
secondArg = list(unknown = 1)),
"All values in 'namesparms' must be one of")
expect_error(linkMultipleVariants(combinedDigestParams = list(fastqForward = 1),
secondArg = list(elementsForward = "CC")),
"Each separate run must contain at least one variable")
expect_error(linkMultipleVariants(combinedDigestParams = list(fastqForward = 1),
secondArg = list(elementsForward = "V",
elementsReverse = "V")),
"A separate run can not have variable sequences in both")
expect_error(linkMultipleVariants(combinedDigestParams = list(fastqForward = 1),
secondArg = list(elementsForward = "VV")),
"A separate run can have at most one variable segment")
## Works with correct input
## ------------------------------------------------------------------------
## Read truth
truth <- readRDS(system.file("extdata", "multipleVariableRegions_truth.rds",
package = "mutscan"))
verbose <- FALSE
## ------------------------------------------------------------------------
## Don't filter by mutations in constant sequence
res <- linkMultipleVariants(
combinedDigestParams = list(
fastqForward = system.file("extdata", "multipleVariableRegions_R1.fastq.gz",
package = "mutscan"),
fastqReverse = system.file("extdata", "multipleVariableRegions_R2.fastq.gz",
package = "mutscan"),
elementsForward = "CVCVCV", elementLengthsForward = c(6, 24, 10, 30, 10, -1),
elementsReverse = "CVCV", elementLengthsReverse = c(6, 40, 10, -1),
mergeForwardReverse = TRUE, minOverlap = 20,
maxOverlap = 30, maxFracMismatchOverlap = 0,
revComplForward = FALSE, revComplReverse = TRUE,
avePhredMinForward = 20, avePhredMinReverse = 20,
verbose = verbose),
barcode = list(
fastqForward = system.file("extdata", "multipleVariableRegions_R1.fastq.gz",
package = "mutscan"),
elementsForward = "CVCSCS", elementLengthsForward = c(6, 24, 10, 30, 10, -1),
avePhredMinForward = 20,
collapseMaxDist = 1, collapseMinScore = 1, collapseMinRatio = 1,
verbose = verbose),
V2 = list(
fastqForward = system.file("extdata", "multipleVariableRegions_R1.fastq.gz",
package = "mutscan"),
fastqReverse = system.file("extdata", "multipleVariableRegions_R2.fastq.gz",
package = "mutscan"),
elementsForward = "CSCVCS", elementLengthsForward = c(6, 24, 10, 30, 10, -1),
elementsReverse = "CSCV", elementLengthsReverse = c(6, 40, 10, -1),
mergeForwardReverse = TRUE, minOverlap = 10,
maxOverlap = 20, maxFracMismatchOverlap = 0,
revComplForward = FALSE, revComplReverse = TRUE,
avePhredMinForward = 20, avePhredMinReverse = 20,
wildTypeForward = truth$WTV2,
nbrMutatedCodonsMaxForward = -1, nbrMutatedBasesMaxForward = 1,
forbiddenMutatedCodonsForward = "", collapseToWTForward = FALSE,
verbose = verbose, useTreeWTmatch = TRUE),
V3 = list(
fastqForward = system.file("extdata", "multipleVariableRegions_R1.fastq.gz",
package = "mutscan"),
fastqReverse = system.file("extdata", "multipleVariableRegions_R2.fastq.gz",
package = "mutscan"),
elementsForward = "CSCSCV", elementLengthsForward = c(6, 24, 10, 30, 10, -1),
elementsReverse = "CVCS", elementLengthsReverse = c(6, 40, 10, -1),
mergeForwardReverse = TRUE, minOverlap = 5,
maxOverlap = 15, maxFracMismatchOverlap = 0,
revComplForward = FALSE, revComplReverse = TRUE,
avePhredMinForward = 20, avePhredMinReverse = 20,
wildTypeForward = truth$WTV3,
nbrMutatedCodonsMaxForward = -1, nbrMutatedBasesMaxForward = 1,
forbiddenMutatedCodonsForward = "", collapseToWTForward = FALSE,
verbose = verbose, useTreeWTmatch = TRUE)
)
## Filter out only reads with N/deletions in the variable sequence
keep <- !grepl("N|del", truth$truth$status)
## Truth
correct <- truth$truth[keep, ] %>%
dplyr::group_by(trueBarcode, trueV2, trueV3) %>% dplyr::tally() %>%
dplyr::arrange(dplyr::desc(n), trueBarcode, trueV2, trueV3)
## Obs
obs <- res$countAggregated %>% dplyr::arrange(desc(nbrReads), barcode, V2, V3)
expect_equal(sum(obs$nbrReads), sum(keep))
expect_equal(correct$trueBarcode, obs$barcode)
expect_equal(correct$trueV2, obs$V2)
expect_equal(correct$trueV3, obs$V3)
expect_equal(correct$n, obs$nbrReads)
expect_equal(res$outCombined$filterSummary[, "f4_nbrNoValidOverlap"],
sum(grepl("del", truth$truth$status))) ## del
expect_equal(res$outCombined$filterSummary[, "f6_nbrTooManyNinVar"],
sum(grepl("N", truth$truth$status))) ## N
expect_equal(res$outCombined$filterSummary[, "nbrRetained"],
sum(!grepl("N|del", truth$truth$status)))
expect_equal(res$filtSeparate$barcode[, "f6_nbrTooManyNinVar"],
sum(grepl("V1N", truth$truth$status)))
expect_equal(res$filtSeparate$barcode[, "nbrRetained"],
sum(!grepl("V1N", truth$truth$status)))
expect_equal(res$filtSeparate$V2[, "f4_nbrNoValidOverlap"],
sum(grepl("del", truth$truth$status)))
expect_equal(res$filtSeparate$V2[, "nbrRetained"],
sum(!grepl("del", truth$truth$status)))
expect_equal(res$filtSeparate$V3[, "f4_nbrNoValidOverlap"],
sum(grepl("del", truth$truth$status)))
expect_equal(res$filtSeparate$V3[, "nbrRetained"],
sum(!grepl("del", truth$truth$status)))
## ------------------------------------------------------------------------
## Filter out mutations in constant sequences
res <- linkMultipleVariants(
combinedDigestParams = list(
fastqForward = system.file("extdata", "multipleVariableRegions_R1.fastq.gz",
package = "mutscan"),
fastqReverse = system.file("extdata", "multipleVariableRegions_R2.fastq.gz",
package = "mutscan"),
elementsForward = "CVCVCV", elementLengthsForward = c(6, 24, 10, 30, 10, -1),
elementsReverse = "CVCV", elementLengthsReverse = c(6, 40, 10, -1),
mergeForwardReverse = TRUE, minOverlap = 20,
maxOverlap = 30, maxFracMismatchOverlap = 0,
revComplForward = FALSE, revComplReverse = TRUE,
constantForward = truth$constFwd,
constantReverse = truth$constRev,
constantMaxDistForward = 0,
constantMaxDistReverse = 0,
avePhredMinForward = 20, avePhredMinReverse = 20,
verbose = verbose),
barcode = list(
fastqForward = system.file("extdata", "multipleVariableRegions_R1.fastq.gz",
package = "mutscan"),
elementsForward = "CVCSCS", elementLengthsForward = c(6, 24, 10, 30, 10, -1),
constantForward = truth$constFwd,
constantMaxDistForward = 0,
avePhredMinForward = 20,
collapseMaxDist = 1, collapseMinScore = 1, collapseMinRatio = 1,
verbose = verbose),
V2 = list(
fastqForward = system.file("extdata", "multipleVariableRegions_R1.fastq.gz",
package = "mutscan"),
fastqReverse = system.file("extdata", "multipleVariableRegions_R2.fastq.gz",
package = "mutscan"),
elementsForward = "CSCVCS", elementLengthsForward = c(6, 24, 10, 30, 10, -1),
elementsReverse = "CSCV", elementLengthsReverse = c(6, 40, 10, -1),
mergeForwardReverse = TRUE, minOverlap = 10,
maxOverlap = 20, maxFracMismatchOverlap = 0,
revComplForward = FALSE, revComplReverse = TRUE,
constantForward = truth$constFwd,
constantReverse = truth$constRev,
constantMaxDistForward = 0,
constantMaxDistReverse = 0,
avePhredMinForward = 20, avePhredMinReverse = 20,
wildTypeForward = truth$WTV2,
nbrMutatedCodonsMaxForward = -1, nbrMutatedBasesMaxForward = 1,
forbiddenMutatedCodonsForward = "", collapseToWTForward = FALSE,
verbose = verbose, useTreeWTmatch = TRUE),
V3 = list(
fastqForward = system.file("extdata", "multipleVariableRegions_R1.fastq.gz",
package = "mutscan"),
fastqReverse = system.file("extdata", "multipleVariableRegions_R2.fastq.gz",
package = "mutscan"),
elementsForward = "CSCSCV", elementLengthsForward = c(6, 24, 10, 30, 10, -1),
elementsReverse = "CVCS", elementLengthsReverse = c(6, 40, 10, -1),
mergeForwardReverse = TRUE, minOverlap = 5,
maxOverlap = 15, maxFracMismatchOverlap = 0,
revComplForward = FALSE, revComplReverse = TRUE,
constantForward = truth$constFwd,
constantReverse = truth$constRev,
constantMaxDistForward = 0,
constantMaxDistReverse = 0,
avePhredMinForward = 20, avePhredMinReverse = 20,
wildTypeForward = truth$WTV3,
nbrMutatedCodonsMaxForward = -1, nbrMutatedBasesMaxForward = 1,
forbiddenMutatedCodonsForward = "", collapseToWTForward = FALSE,
verbose = verbose, useTreeWTmatch = TRUE)
)
## Filter out reads with N/deletions in the variable sequence, or mutations in constant
keep <- !grepl("C.*mut|N|del", truth$truth$status)
## Truth
correct <- truth$truth[keep, ] %>%
dplyr::group_by(trueBarcode, trueV2, trueV3) %>% dplyr::tally() %>%
dplyr::arrange(dplyr::desc(n), trueBarcode, trueV2, trueV3)
## Obs
obs <- res$countAggregated %>% dplyr::arrange(desc(nbrReads), barcode, V2, V3)
expect_equal(sum(obs$nbrReads), sum(keep))
expect_equal(correct$trueBarcode, obs$barcode)
expect_equal(correct$trueV2, obs$V2)
expect_equal(correct$trueV3, obs$V3)
expect_equal(correct$n, obs$nbrReads)
## first filter out reads with deletion -> no valid overlap
## then reads with N in barcode -> too many N
## then reads with mutation in constant
expect_equal(res$outCombined$filterSummary[, "f4_nbrNoValidOverlap"],
sum(grepl("del", truth$truth$status)))
expect_equal(res$outCombined$filterSummary[, "f6_nbrTooManyNinVar"],
sum(grepl("N", truth$truth$status)))
expect_equal(res$outCombined$filterSummary[, "f12_nbrTooManyMutConstant"],
sum(grepl("C.*mut", truth$truth$status) &
!grepl("N", truth$truth$status) &
!grepl("del", truth$truth$status)))
expect_equal(res$outCombined$filterSummary[, "nbrRetained"],
sum(!grepl("C.*mut|N|del", truth$truth$status)))
expect_equal(res$filtSeparate$barcode[, "f6_nbrTooManyNinVar"],
sum(grepl("V1N", truth$truth$status)))
expect_equal(res$filtSeparate$barcode[, "f12_nbrTooManyMutConstant"],
sum(grepl("C[1-3]mut|del", truth$truth$status) &
!grepl("V1N", truth$truth$status)))
expect_equal(res$filtSeparate$barcode[, "nbrRetained"],
sum(!grepl("V1N|C[1-3]mut|del", truth$truth$status)))
expect_equal(res$filtSeparate$V2[, "f4_nbrNoValidOverlap"],
sum(grepl("del", truth$truth$status)))
expect_equal(res$filtSeparate$V2[, "f12_nbrTooManyMutConstant"],
sum(grepl("C.*mut", truth$truth$status) &
!grepl("del", truth$truth$status)))
expect_equal(res$filtSeparate$V2[, "nbrRetained"],
sum(!grepl("C.*mut|del", truth$truth$status)))
expect_equal(res$filtSeparate$V3[, "f4_nbrNoValidOverlap"],
sum(grepl("del", truth$truth$status)))
expect_equal(res$filtSeparate$V3[, "f12_nbrTooManyMutConstant"],
sum(grepl("C.*mut", truth$truth$status) &
!grepl("del", truth$truth$status)))
expect_equal(res$filtSeparate$V3[, "nbrRetained"],
sum(!grepl("C.*mut|del", truth$truth$status)))
## ------------------------------------------------------------------------
## Collapse to WT
res <- linkMultipleVariants(
combinedDigestParams = list(
fastqForward = system.file("extdata", "multipleVariableRegions_R1.fastq.gz",
package = "mutscan"),
fastqReverse = system.file("extdata", "multipleVariableRegions_R2.fastq.gz",
package = "mutscan"),
elementsForward = "CVCVCV", elementLengthsForward = c(6, 24, 10, 30, 10, -1),
elementsReverse = "CVCV", elementLengthsReverse = c(6, 40, 10, -1),
mergeForwardReverse = TRUE, minOverlap = 20,
maxOverlap = 30, maxFracMismatchOverlap = 0,
revComplForward = FALSE, revComplReverse = TRUE,
avePhredMinForward = 20, avePhredMinReverse = 20,
verbose = verbose),
barcode = list(
fastqForward = system.file("extdata", "multipleVariableRegions_R1.fastq.gz",
package = "mutscan"),
elementsForward = "CVCSCS", elementLengthsForward = c(6, 24, 10, 30, 10, -1),
avePhredMinForward = 20,
collapseMaxDist = 1, collapseMinScore = 1, collapseMinRatio = 1,
verbose = verbose),
V2 = list(
fastqForward = system.file("extdata", "multipleVariableRegions_R1.fastq.gz",
package = "mutscan"),
fastqReverse = system.file("extdata", "multipleVariableRegions_R2.fastq.gz",
package = "mutscan"),
elementsForward = "CSCVCS", elementLengthsForward = c(6, 24, 10, 30, 10, -1),
elementsReverse = "CSCV", elementLengthsReverse = c(6, 40, 10, -1),
mergeForwardReverse = TRUE, minOverlap = 10,
maxOverlap = 20, maxFracMismatchOverlap = 0,
revComplForward = FALSE, revComplReverse = TRUE,
avePhredMinForward = 20, avePhredMinReverse = 20,
wildTypeForward = truth$WTV2,
nbrMutatedCodonsMaxForward = -1, nbrMutatedBasesMaxForward = 1,
forbiddenMutatedCodonsForward = "", collapseToWTForward = TRUE,
verbose = verbose, useTreeWTmatch = TRUE),
V3 = list(
fastqForward = system.file("extdata", "multipleVariableRegions_R1.fastq.gz",
package = "mutscan"),
fastqReverse = system.file("extdata", "multipleVariableRegions_R2.fastq.gz",
package = "mutscan"),
elementsForward = "CSCSCV", elementLengthsForward = c(6, 24, 10, 30, 10, -1),
elementsReverse = "CVCS", elementLengthsReverse = c(6, 40, 10, -1),
mergeForwardReverse = TRUE, minOverlap = 5,
maxOverlap = 15, maxFracMismatchOverlap = 0,
revComplForward = FALSE, revComplReverse = TRUE,
avePhredMinForward = 20, avePhredMinReverse = 20,
wildTypeForward = truth$WTV3,
nbrMutatedCodonsMaxForward = -1, nbrMutatedBasesMaxForward = 1,
forbiddenMutatedCodonsForward = "", collapseToWTForward = TRUE,
verbose = verbose, useTreeWTmatch = TRUE)
)
## Filter out only reads with N/deletions in the variable sequence
keep <- !grepl("N|del", truth$truth$status)
## Truth
correct <- truth$truth[keep, ] %>%
dplyr::mutate(trueV2 = gsub("\\..*", "", trueV2),
trueV3 = gsub("\\..*", "", trueV3)) %>%
dplyr::group_by(trueBarcode, trueV2, trueV3) %>% dplyr::tally() %>%
dplyr::arrange(dplyr::desc(n), trueBarcode, trueV2, trueV3)
## Obs
obs <- res$countAggregated %>% dplyr::arrange(desc(nbrReads), barcode, V2, V3)
expect_equal(sum(obs$nbrReads), sum(keep))
expect_equal(correct$trueBarcode, obs$barcode)
expect_equal(correct$trueV2, obs$V2)
expect_equal(correct$trueV3, obs$V3)
expect_equal(correct$n, obs$nbrReads)
expect_equal(res$outCombined$filterSummary[, "f4_nbrNoValidOverlap"],
sum(grepl("del", truth$truth$status))) ## del
expect_equal(res$outCombined$filterSummary[, "f6_nbrTooManyNinVar"],
sum(grepl("N", truth$truth$status))) ## N
expect_equal(res$outCombined$filterSummary[, "nbrRetained"],
sum(!grepl("N|del", truth$truth$status)))
expect_equal(res$filtSeparate$barcode[, "f6_nbrTooManyNinVar"],
sum(grepl("V1N", truth$truth$status)))
expect_equal(res$filtSeparate$barcode[, "nbrRetained"],
sum(!grepl("V1N", truth$truth$status)))
expect_equal(res$filtSeparate$V2[, "f4_nbrNoValidOverlap"],
sum(grepl("del", truth$truth$status)))
expect_equal(res$filtSeparate$V2[, "nbrRetained"],
sum(!grepl("del", truth$truth$status)))
expect_equal(res$filtSeparate$V3[, "f4_nbrNoValidOverlap"],
sum(grepl("del", truth$truth$status)))
expect_equal(res$filtSeparate$V3[, "nbrRetained"],
sum(!grepl("del", truth$truth$status)))
## ------------------------------------------------------------------------
## Don't merge fwd and rev
res <- linkMultipleVariants(
combinedDigestParams = list(
fastqForward = system.file("extdata", "multipleVariableRegions_R1.fastq.gz",
package = "mutscan"),
fastqReverse = system.file("extdata", "multipleVariableRegions_R2.fastq.gz",
package = "mutscan"),
elementsForward = "CVCVCS", elementLengthsForward = c(6, 24, 10, 30, 10, -1),
elementsReverse = "CVCS", elementLengthsReverse = c(6, 40, 10, -1),
mergeForwardReverse = FALSE,
revComplForward = FALSE, revComplReverse = TRUE,
avePhredMinForward = 20, avePhredMinReverse = 20,
verbose = verbose),
barcode = list(
fastqForward = system.file("extdata", "multipleVariableRegions_R1.fastq.gz",
package = "mutscan"),
elementsForward = "CVCSCS", elementLengthsForward = c(6, 24, 10, 30, 10, -1),
avePhredMinForward = 20,
collapseMaxDist = 1, collapseMinScore = 1, collapseMinRatio = 1,
verbose = verbose),
V2 = list(
fastqForward = system.file("extdata", "multipleVariableRegions_R1.fastq.gz",
package = "mutscan"),
elementsForward = "CSCVCS", elementLengthsForward = c(6, 24, 10, 30, 10, -1),
mergeForwardReverse = FALSE,
revComplForward = FALSE, revComplReverse = TRUE,
avePhredMinForward = 20, avePhredMinReverse = 20,
wildTypeForward = truth$WTV2,
nbrMutatedCodonsMaxForward = -1, nbrMutatedBasesMaxForward = 1,
forbiddenMutatedCodonsForward = "", collapseToWTForward = FALSE,
verbose = verbose, useTreeWTmatch = TRUE),
V3 = list(
fastqForward = system.file("extdata", "multipleVariableRegions_R2.fastq.gz",
package = "mutscan"),
elementsForward = "CVCS", elementLengthsForward = c(6, 40, 10, -1),
mergeForwardReverse = FALSE,
revComplForward = TRUE,
avePhredMinForward = 20, avePhredMinReverse = 20,
wildTypeForward = truth$WTV3,
nbrMutatedCodonsMaxForward = -1, nbrMutatedBasesMaxForward = 1,
forbiddenMutatedCodonsForward = "", collapseToWTForward = FALSE,
verbose = verbose, useTreeWTmatch = TRUE)
)
## Filter out only reads with N/deletions in the variable sequence
keep <- !grepl("N|del", truth$truth$status)
## Truth
correct <- truth$truth[keep, ] %>%
dplyr::group_by(trueBarcode, trueV2, trueV3) %>% dplyr::tally() %>%
dplyr::arrange(dplyr::desc(n), trueBarcode, trueV2, trueV3)
## Obs
obs <- res$countAggregated %>% dplyr::arrange(desc(nbrReads), barcode, V2, V3)
expect_equal(sum(obs$nbrReads), sum(keep))
expect_equal(correct$trueBarcode, obs$barcode)
expect_equal(correct$trueV2, obs$V2)
expect_equal(correct$trueV3, obs$V3)
expect_equal(correct$n, obs$nbrReads)
expect_equal(res$outCombined$filterSummary[, "f6_nbrTooManyNinVar"],
sum(grepl("N", truth$truth$status)))
expect_equal(res$outCombined$filterSummary[, "nbrRetained"],
sum(!grepl("N", truth$truth$status)))
expect_equal(res$filtSeparate$barcode[, "f6_nbrTooManyNinVar"],
sum(grepl("V1N", truth$truth$status)))
expect_equal(res$filtSeparate$barcode[, "nbrRetained"],
sum(!grepl("V1N", truth$truth$status)))
expect_equal(res$filtSeparate$V2[, "f10b_nbrTooManyMutBases"],
sum(grepl("del", truth$truth$status)))
expect_equal(res$filtSeparate$V2[, "nbrRetained"],
sum(!grepl("del", truth$truth$status)))
expect_equal(res$filtSeparate$V3[, "nbrRetained"], 100)
## ------------------------------------------------------------------------
## Don't allow any mutations
res <- linkMultipleVariants(
combinedDigestParams = list(
fastqForward = system.file("extdata", "multipleVariableRegions_R1.fastq.gz",
package = "mutscan"),
fastqReverse = system.file("extdata", "multipleVariableRegions_R2.fastq.gz",
package = "mutscan"),
elementsForward = "CVCVCV", elementLengthsForward = c(6, 24, 10, 30, 10, -1),
elementsReverse = "CVCV", elementLengthsReverse = c(6, 40, 10, -1),
mergeForwardReverse = TRUE, minOverlap = 20,
maxOverlap = 30, maxFracMismatchOverlap = 0,
revComplForward = FALSE, revComplReverse = TRUE,
constantForward = truth$constFwd,
constantReverse = truth$constRev,
constantMaxDistForward = 0,
constantMaxDistReverse = 0,
avePhredMinForward = 20, avePhredMinReverse = 20,
verbose = verbose),
barcode = list(
fastqForward = system.file("extdata", "multipleVariableRegions_R1.fastq.gz",
package = "mutscan"),
elementsForward = "CVCSCS", elementLengthsForward = c(6, 24, 10, 30, 10, -1),
constantForward = truth$constFwd,
constantMaxDistForward = 0,
avePhredMinForward = 20,
collapseMaxDist = 0, collapseMinScore = 1, collapseMinRatio = 1,
verbose = verbose),
V2 = list(
fastqForward = system.file("extdata", "multipleVariableRegions_R1.fastq.gz",
package = "mutscan"),
fastqReverse = system.file("extdata", "multipleVariableRegions_R2.fastq.gz",
package = "mutscan"),
elementsForward = "CSCVCS", elementLengthsForward = c(6, 24, 10, 30, 10, -1),
elementsReverse = "CSCV", elementLengthsReverse = c(6, 40, 10, -1),
mergeForwardReverse = TRUE, minOverlap = 10,
maxOverlap = 20, maxFracMismatchOverlap = 0,
revComplForward = FALSE, revComplReverse = TRUE,
constantForward = truth$constFwd,
constantReverse = truth$constRev,
constantMaxDistForward = 0,
constantMaxDistReverse = 0,
avePhredMinForward = 20, avePhredMinReverse = 20,
wildTypeForward = truth$WTV2,
nbrMutatedCodonsMaxForward = -1, nbrMutatedBasesMaxForward = 0,
forbiddenMutatedCodonsForward = "", collapseToWTForward = FALSE,
verbose = verbose, useTreeWTmatch = TRUE),
V3 = list(
fastqForward = system.file("extdata", "multipleVariableRegions_R1.fastq.gz",
package = "mutscan"),
fastqReverse = system.file("extdata", "multipleVariableRegions_R2.fastq.gz",
package = "mutscan"),
elementsForward = "CSCSCV", elementLengthsForward = c(6, 24, 10, 30, 10, -1),
elementsReverse = "CVCS", elementLengthsReverse = c(6, 40, 10, -1),
mergeForwardReverse = TRUE, minOverlap = 5,
maxOverlap = 15, maxFracMismatchOverlap = 0,
revComplForward = FALSE, revComplReverse = TRUE,
constantForward = truth$constFwd,
constantReverse = truth$constRev,
constantMaxDistForward = 0,
constantMaxDistReverse = 0,
avePhredMinForward = 20, avePhredMinReverse = 20,
wildTypeForward = truth$WTV3,
nbrMutatedCodonsMaxForward = -1, nbrMutatedBasesMaxForward = 0,
forbiddenMutatedCodonsForward = "", collapseToWTForward = FALSE,
verbose = verbose, useTreeWTmatch = TRUE)
)
## Filter out reads with N/deletions in the variable sequence, or mutations in constant
keep <- !grepl("C.*mut|N|del|V2|V3", truth$truth$status)
## Truth
correct <- truth$truth[keep, ] %>%
dplyr::group_by(obsBarcode, trueV2, trueV3) %>% dplyr::tally() %>%
dplyr::arrange(dplyr::desc(n), obsBarcode, trueV2, trueV3)
## Obs
obs <- res$countAggregated %>% dplyr::arrange(desc(nbrReads), barcode, V2, V3)
expect_equal(sum(obs$nbrReads), sum(keep))
expect_equal(correct$obsBarcode, obs$barcode)
expect_equal(correct$trueV2, obs$V2)
expect_equal(correct$trueV3, obs$V3)
expect_equal(correct$n, obs$nbrReads)
expect_equal(res$outCombined$filterSummary[, "f4_nbrNoValidOverlap"],
sum(grepl("del", truth$truth$status)))
expect_equal(res$outCombined$filterSummary[, "f6_nbrTooManyNinVar"],
sum(grepl("N", truth$truth$status)))
expect_equal(res$outCombined$filterSummary[, "f12_nbrTooManyMutConstant"],
sum(grepl("C.*mut", truth$truth$status) &
!grepl("N", truth$truth$status) &
!grepl("del", truth$truth$status)))
expect_equal(res$outCombined$filterSummary[, "nbrRetained"],
sum(!grepl("C.*mut|N|del", truth$truth$status)))
expect_equal(res$filtSeparate$barcode[, "f6_nbrTooManyNinVar"],
sum(grepl("V1N", truth$truth$status)))
expect_equal(res$filtSeparate$barcode[, "f12_nbrTooManyMutConstant"],
sum(grepl("C[1-3]mut|del", truth$truth$status) &
!grepl("V1N", truth$truth$status)))
expect_equal(res$filtSeparate$barcode[, "nbrRetained"],
sum(!grepl("V1N|C[1-3]mut|del", truth$truth$status)))
expect_equal(res$filtSeparate$V2[, "f4_nbrNoValidOverlap"],
sum(grepl("del", truth$truth$status)))
expect_equal(res$filtSeparate$V2[, "f10b_nbrTooManyMutBases"],
sum(grepl("V2v[0-9]\\.", truth$truth$status) &
!grepl("del", truth$truth$status)))
expect_equal(res$filtSeparate$V2[, "f12_nbrTooManyMutConstant"],
sum(grepl("C.*mut", truth$truth$status) &
!grepl("del", truth$truth$status) &
!grepl("V2v[0-9]\\.", truth$truth$status)))
expect_equal(res$filtSeparate$V2[, "nbrRetained"],
sum(!grepl("C.*mut|del|V2v[0-9]\\.", truth$truth$status)))
expect_equal(res$filtSeparate$V3[, "f4_nbrNoValidOverlap"],
sum(grepl("del", truth$truth$status)))
expect_equal(res$filtSeparate$V3[, "f10b_nbrTooManyMutBases"],
sum(grepl("V3\\.", truth$truth$status) &
!grepl("del", truth$truth$status)))
expect_equal(res$filtSeparate$V3[, "f12_nbrTooManyMutConstant"],
sum(grepl("C.*mut", truth$truth$status) &
!grepl("del", truth$truth$status) &
!grepl("V3\\.", truth$truth$status)))
expect_equal(res$filtSeparate$V3[, "nbrRetained"],
sum(!grepl("C.*mut|del|V3\\.", truth$truth$status)))
})
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