Nothing
tests/testthat/test.5_sm.R
In msPurity: Automated Evaluation of Precursor Ion Purity for Mass Spectrometry Based Fragmentation in Metabolomics
context ("checking spectral matching functions ")
# test_that("checking spectral matching functions (spectral_matching)", {
# print ("\n")
# print("########################################################")
# print("## Testing spectral matching (spectral_matching) ##")
# print("########################################################")
# td <- tempdir()
#
# #msmsPths <- list.files(system.file("extdata", "lcms", "mzML", package="msPurityData"), full.names = TRUE, pattern = "MSMS")
# #xset <- xcms::xcmsSet(msmsPths)
# #xset <- xcms::group(xset)
# #xset <- xcms::retcor(xset)
# #xset <- xcms::group(xset)
#
# #pa <- purityA(msmsPths)
# #pa <- frag4feature(pa, xset)
# #pa <- averageAllFragSpectra(pa)
#
# #q_copyDbPth <- create_database(pa, xset = xset, out_dir = td)
# q_dbPth <- system.file("extdata", "tests", "db", "create_database_example.sqlite", package="msPurity")
# q_copyDbPth <- file.path(td, paste0(format(Sys.time(), "%Y-%m-%d-%I%M%S"), 'copy_OLD_spectral_matching.sqlite'))
# file.copy(from = q_dbPth, to=q_copyDbPth)
#
# result <- spectral_matching(q_copyDbPth, spectra_type_q = 'av_all', match_alg = 'dpc')
#
# expect_equal(result$xcms_summary_df$grpid, c(12, 27, 33, 42, 49, 65, 76, 213, 351))
# expect_equal(result$xcms_summary_df$best_name, c("proline", "Isoleucine", "N-methylnicotinate",
# "Acetylcholine", "Oxypurinol", "alpha-Methyl-DL-histidine",
# "Tyrosine", "Aspartame", "Doxazosin" ))
# expect_equal(round(as.numeric(result$xcms_summary_df$best_median_score), 3),
# c(1.000, 0.929, 0.988, 0.949, 0.800, 0.922, 0.707, 0.718, 0.976))
#
#
# })
test_that("checking spectral matching functions (spectralMatching) query vs library", {
print ("\n")
print("########################################################")
print("## Testing spectral matching (spectralMatching) qvl ##")
print("########################################################")
# msmsPths <- list.files(system.file("extdata", "lcms", "mzML", package="msPurityData"), full.names = TRUE, pattern = "MSMS")
# xset <- xcms::xcmsSet(msmsPths)
# xset <- xcms::group(xset)
# xset <- xcms::retcor(xset)
# xset <- xcms::group(xset)
#
# pa <- purityA(msmsPths)
# pa <- frag4feature(pa, xset)
# pa <- filterFragSpectra(pa, allfrag=TRUE, plim=0, ilim = 0, snr = 0)
# pa <- averageIntraFragSpectra(pa)
# pa <- averageInterFragSpectra(pa)
# pa <- averageAllFragSpectra(pa)
# q_dbPth <- createDatabase(pa, xset, metadata=list('polarity'='positive', 'instrument'='Q-Exactive'))
#
td <- tempdir()
q_dbPth <- system.file("extdata", "tests", "db", "createDatabase_example.sqlite", package="msPurity")
rid <- paste0(paste0(sample(LETTERS, 5, TRUE), collapse=""), paste0(sample(9999, 1, TRUE), collapse=""), ".sqlite")
sm_out_pth <- file.path(td, rid)
result <- spectralMatching(q_dbPth, q_xcmsGroups = c(12, 27), cores=1, l_accessions=c('CCMSLIB00000577898','CE000616'),
q_spectraTypes = 'av_all',
updateDb = TRUE,
copyDb = TRUE,
outPth = sm_out_pth)
expect_equal(result$xcmsMatchedResults$grpid, c(12,27))
expect_equal(result$xcmsMatchedResults$library_accession, c("CCMSLIB00000577898", "CE000616"))
expect_equal(result$xcmsMatchedResults$inchikey, c("ONIBWKKTOPOVIA-UHFFFAOYSA-N", "AGPKZVBTJJNPAG-UHFFFAOYSA-N"))
expect_equal(round(as.numeric(result$xcmsMatchedResults$dpc),3), c( 0.879, 0.941))
expect_equal(round(as.numeric(result$xcmsMatchedResults$rdpc),3), c( 0.881, 0.941))
expect_equal(round(as.numeric(result$xcmsMatchedResults$cdpc),3), c( 0.857, 0.896))
expect_equal(round(as.numeric(result$xcmsMatchedResults$mcount),3), c( 2, 1))
expect_equal(round(as.numeric(result$xcmsMatchedResults$allcount),3), c( 23, 20))
})
test_that("checking spectral matching functions (spectralMatching) library vs library", {
print ("\n")
print("########################################################")
print("## Testing spectral matching (spectralMatching) lvl ##")
print("########################################################")
# q_purity=NA
# q_ppmProd=10
# q_ppmPrec=5
# q_raThres=NA
# q_pol=NA
# q_instrumentTypes=NA
# q_instrument=NA
# q_sources=NA
# q_spectraTypes=NA
# q_pids=c(1,2,3)
# q_rtrange=c(NA, NA)
# q_spectraFilter=TRUE
# q_xcmsGroups=NA
# q_accessions=NA
#
# l_purity=NA
# l_ppmProd=10
# l_ppmPrec=5
# l_raThres=NA
# l_pol=NA
# l_instrumentTypes=NA
# l_instrument=NA
# l_sources=NA
# l_spectraTypes=NA
# l_pids=c(1,2,3)
# l_rtrange=c(NA, NA)
# l_spectraFilter=FALSE
# l_xcmsGroups=NA
# l_accessions=NA
# usePrecursors=TRUE
# raW=0.5
# mzW=2
# rttol=NA
# updateDb = TRUE
# copyDb = TRUE
# outPth = sm_out_pth
td <- tempdir()
rid <- paste0(paste0(sample(LETTERS, 5, TRUE), collapse=""), paste0(sample(9999, 1, TRUE), collapse=""), ".sqlite")
sm_out_pth <- file.path(td, rid)
q_dbPth <- system.file("extdata", "library_spectra", "library_spectra.db", package="msPurityData")
l_dbPth <- system.file("extdata", "library_spectra", "library_spectra.db", package="msPurityData")
result <- spectralMatching(q_dbPth=q_dbPth,
l_dbPth=l_dbPth,
q_pids = c(1,2,3),
q_spectraTypes = NA,
cores=1,
q_pol = NA,
l_pids = c(1,2,3),
l_spectraTypes = NA,
updateDb = TRUE,
copyDb = TRUE,
outPth = sm_out_pth)
matched <- result$matchedResults
expect_equal(matched$lpid, c(1,2,3))
expect_equal(matched$dpc, c(1,1,1))
expect_equal(matched$rdpc, c(1,1,1))
expect_equal(matched$cdpc, c(1,1,1))
expect_equal(matched$mcount, c(43,9,321))
expect_equal(matched$allcount, c(43,9,321))
expect_equal(matched$library_accession, c("CCMSLIB00000001577", "CCMSLIB00000001666", "CCMSLIB00000004593"))
expect_equal(matched$library_entry_name, c("Carmaphycin B", "CarmaphycinA_enone", "MaprotilineHCl"))
expect_equal(matched$qpid, c(1,2,3))
})
test_that("checking spectral matching functions (spectralMatching) query vs query", {
print ("\n")
print("########################################################")
print("## Testing spectral matching (spectralMatching) qvq ##")
print("########################################################")
td <- tempdir()
q_dbPth <- system.file("extdata", "tests", "db", "createDatabase_example.sqlite", package="msPurity")
l_dbPth <- system.file("extdata", "tests", "db", "createDatabase_example.sqlite", package="msPurity")
rid <- paste0(paste0(sample(LETTERS, 5, TRUE), collapse=""), paste0(sample(9999, 1, TRUE), collapse=""), ".sqlite")
sm_out_pth <- file.path(td, rid)
result <- spectralMatching(q_dbPth=q_dbPth,
l_dbPth=l_dbPth,
q_xcmsGroups = c(12, 27),
q_spectraTypes = 'av_all',
q_spectraFilter = TRUE,
q_pol = NA,
l_xcmsGroups = c(12, 27),
l_spectraTypes = 'av_all',
l_pol = NA,
l_spectraFilter = TRUE,
cores=1,
updateDb = TRUE,
copyDb = TRUE,
usePrecursors=TRUE,
outPth = sm_out_pth)
matched <- result$matchedResults
expect_equal(matched$lpid, c(1666, 1670))
expect_equal(matched$qpid, c(1666, 1670))
expect_equal(matched$dpc, c(1,1))
expect_equal(matched$rdpc, c(1,1))
expect_equal(matched$cdpc, c(1,1))
expect_equal(matched$mcount, c(3, 1))
expect_equal(matched$allcount, c(3, 1))
xcmsMatchedResults <- result$xcmsMatchedResults
expect_equal(xcmsMatchedResults$pid, c(1666, 1670))
expect_equal(xcmsMatchedResults$lpid, c(1666, 1670))
expect_equal(xcmsMatchedResults$grpid, c(12, 27))
})
test_that("checking spectral matching functions (spectralMatching) query(scans) vs library", {
print ("\n")
print("#################################################################")
print("## Testing spectral matching (spectralMatching) q(scan) v q ##")
print("#################################################################")
td <- tempdir()
q_dbPth <- system.file("extdata", "tests", "db", "createDatabase_example.sqlite", package="msPurity")
rid <- paste0(paste0(sample(LETTERS, 5, TRUE), collapse=""), paste0(sample(9999, 1, TRUE), collapse=""), ".sqlite")
sm_out_pth <- file.path(td, rid)
result <- spectralMatching(q_dbPth, q_xcmsGroups = c(12, 27), cores=1, l_accessions=c('CCMSLIB00000577898','CE000616'),
q_spectraTypes = 'scan',
updateDb = TRUE,
copyDb = TRUE,
outPth = sm_out_pth)
matched <- result$matchedResults
expect_equal(matched$lpid, c(5325, 5325, 5325, 5325, 5325, 5325, 53807, 53807, 53807, 53807, 53807, 53807))
expect_equal(matched$qpid, c(226, 281, 336, 1110, 1166, 1055, 509, 394, 451, 1220, 1275, 1330))
expect_equal(round(matched$dpc,2), c(0.14, 0.03, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0))
expect_equal(round(matched$rdpc,2), c( 0.87 , 0.87 ,NaN ,NaN ,NaN ,NaN ,NaN ,NaN ,NaN ,NaN ,NaN ,NaN ))
expect_equal(round(matched$cdpc,2), c(0.13, 0.03, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0))
expect_equal(matched$mcount, c(1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0))
expect_equal(matched$allcount, c(34, 46, 56, 53, 37, 43, 34, 59, 30, 24, 40, 29))
xcmsMatchedResults <- result$xcmsMatchedResults
expect_equal(xcmsMatchedResults$grpid, c(12, 12, 12, 12, 12, 12, 27, 27, 27, 27, 27, 27))
})
Try the msPurity package in your browser
Any scripts or data that you put into this service are public.
msPurity documentation built on Jan. 14, 2021, 2:44 a.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.
context ("checking spectral matching functions ")
# test_that("checking spectral matching functions (spectral_matching)", {
# print ("\n")
# print("########################################################")
# print("## Testing spectral matching (spectral_matching) ##")
# print("########################################################")
# td <- tempdir()
#
# #msmsPths <- list.files(system.file("extdata", "lcms", "mzML", package="msPurityData"), full.names = TRUE, pattern = "MSMS")
# #xset <- xcms::xcmsSet(msmsPths)
# #xset <- xcms::group(xset)
# #xset <- xcms::retcor(xset)
# #xset <- xcms::group(xset)
#
# #pa <- purityA(msmsPths)
# #pa <- frag4feature(pa, xset)
# #pa <- averageAllFragSpectra(pa)
#
# #q_copyDbPth <- create_database(pa, xset = xset, out_dir = td)
# q_dbPth <- system.file("extdata", "tests", "db", "create_database_example.sqlite", package="msPurity")
# q_copyDbPth <- file.path(td, paste0(format(Sys.time(), "%Y-%m-%d-%I%M%S"), 'copy_OLD_spectral_matching.sqlite'))
# file.copy(from = q_dbPth, to=q_copyDbPth)
#
# result <- spectral_matching(q_copyDbPth, spectra_type_q = 'av_all', match_alg = 'dpc')
#
# expect_equal(result$xcms_summary_df$grpid, c(12, 27, 33, 42, 49, 65, 76, 213, 351))
# expect_equal(result$xcms_summary_df$best_name, c("proline", "Isoleucine", "N-methylnicotinate",
# "Acetylcholine", "Oxypurinol", "alpha-Methyl-DL-histidine",
# "Tyrosine", "Aspartame", "Doxazosin" ))
# expect_equal(round(as.numeric(result$xcms_summary_df$best_median_score), 3),
# c(1.000, 0.929, 0.988, 0.949, 0.800, 0.922, 0.707, 0.718, 0.976))
#
#
# })
test_that("checking spectral matching functions (spectralMatching) query vs library", {
print ("\n")
print("########################################################")
print("## Testing spectral matching (spectralMatching) qvl ##")
print("########################################################")
# msmsPths <- list.files(system.file("extdata", "lcms", "mzML", package="msPurityData"), full.names = TRUE, pattern = "MSMS")
# xset <- xcms::xcmsSet(msmsPths)
# xset <- xcms::group(xset)
# xset <- xcms::retcor(xset)
# xset <- xcms::group(xset)
#
# pa <- purityA(msmsPths)
# pa <- frag4feature(pa, xset)
# pa <- filterFragSpectra(pa, allfrag=TRUE, plim=0, ilim = 0, snr = 0)
# pa <- averageIntraFragSpectra(pa)
# pa <- averageInterFragSpectra(pa)
# pa <- averageAllFragSpectra(pa)
# q_dbPth <- createDatabase(pa, xset, metadata=list('polarity'='positive', 'instrument'='Q-Exactive'))
#
td <- tempdir()
q_dbPth <- system.file("extdata", "tests", "db", "createDatabase_example.sqlite", package="msPurity")
rid <- paste0(paste0(sample(LETTERS, 5, TRUE), collapse=""), paste0(sample(9999, 1, TRUE), collapse=""), ".sqlite")
sm_out_pth <- file.path(td, rid)
result <- spectralMatching(q_dbPth, q_xcmsGroups = c(12, 27), cores=1, l_accessions=c('CCMSLIB00000577898','CE000616'),
q_spectraTypes = 'av_all',
updateDb = TRUE,
copyDb = TRUE,
outPth = sm_out_pth)
expect_equal(result$xcmsMatchedResults$grpid, c(12,27))
expect_equal(result$xcmsMatchedResults$library_accession, c("CCMSLIB00000577898", "CE000616"))
expect_equal(result$xcmsMatchedResults$inchikey, c("ONIBWKKTOPOVIA-UHFFFAOYSA-N", "AGPKZVBTJJNPAG-UHFFFAOYSA-N"))
expect_equal(round(as.numeric(result$xcmsMatchedResults$dpc),3), c( 0.879, 0.941))
expect_equal(round(as.numeric(result$xcmsMatchedResults$rdpc),3), c( 0.881, 0.941))
expect_equal(round(as.numeric(result$xcmsMatchedResults$cdpc),3), c( 0.857, 0.896))
expect_equal(round(as.numeric(result$xcmsMatchedResults$mcount),3), c( 2, 1))
expect_equal(round(as.numeric(result$xcmsMatchedResults$allcount),3), c( 23, 20))
})
test_that("checking spectral matching functions (spectralMatching) library vs library", {
print ("\n")
print("########################################################")
print("## Testing spectral matching (spectralMatching) lvl ##")
print("########################################################")
# q_purity=NA
# q_ppmProd=10
# q_ppmPrec=5
# q_raThres=NA
# q_pol=NA
# q_instrumentTypes=NA
# q_instrument=NA
# q_sources=NA
# q_spectraTypes=NA
# q_pids=c(1,2,3)
# q_rtrange=c(NA, NA)
# q_spectraFilter=TRUE
# q_xcmsGroups=NA
# q_accessions=NA
#
# l_purity=NA
# l_ppmProd=10
# l_ppmPrec=5
# l_raThres=NA
# l_pol=NA
# l_instrumentTypes=NA
# l_instrument=NA
# l_sources=NA
# l_spectraTypes=NA
# l_pids=c(1,2,3)
# l_rtrange=c(NA, NA)
# l_spectraFilter=FALSE
# l_xcmsGroups=NA
# l_accessions=NA
# usePrecursors=TRUE
# raW=0.5
# mzW=2
# rttol=NA
# updateDb = TRUE
# copyDb = TRUE
# outPth = sm_out_pth
td <- tempdir()
rid <- paste0(paste0(sample(LETTERS, 5, TRUE), collapse=""), paste0(sample(9999, 1, TRUE), collapse=""), ".sqlite")
sm_out_pth <- file.path(td, rid)
q_dbPth <- system.file("extdata", "library_spectra", "library_spectra.db", package="msPurityData")
l_dbPth <- system.file("extdata", "library_spectra", "library_spectra.db", package="msPurityData")
result <- spectralMatching(q_dbPth=q_dbPth,
l_dbPth=l_dbPth,
q_pids = c(1,2,3),
q_spectraTypes = NA,
cores=1,
q_pol = NA,
l_pids = c(1,2,3),
l_spectraTypes = NA,
updateDb = TRUE,
copyDb = TRUE,
outPth = sm_out_pth)
matched <- result$matchedResults
expect_equal(matched$lpid, c(1,2,3))
expect_equal(matched$dpc, c(1,1,1))
expect_equal(matched$rdpc, c(1,1,1))
expect_equal(matched$cdpc, c(1,1,1))
expect_equal(matched$mcount, c(43,9,321))
expect_equal(matched$allcount, c(43,9,321))
expect_equal(matched$library_accession, c("CCMSLIB00000001577", "CCMSLIB00000001666", "CCMSLIB00000004593"))
expect_equal(matched$library_entry_name, c("Carmaphycin B", "CarmaphycinA_enone", "MaprotilineHCl"))
expect_equal(matched$qpid, c(1,2,3))
})
test_that("checking spectral matching functions (spectralMatching) query vs query", {
print ("\n")
print("########################################################")
print("## Testing spectral matching (spectralMatching) qvq ##")
print("########################################################")
td <- tempdir()
q_dbPth <- system.file("extdata", "tests", "db", "createDatabase_example.sqlite", package="msPurity")
l_dbPth <- system.file("extdata", "tests", "db", "createDatabase_example.sqlite", package="msPurity")
rid <- paste0(paste0(sample(LETTERS, 5, TRUE), collapse=""), paste0(sample(9999, 1, TRUE), collapse=""), ".sqlite")
sm_out_pth <- file.path(td, rid)
result <- spectralMatching(q_dbPth=q_dbPth,
l_dbPth=l_dbPth,
q_xcmsGroups = c(12, 27),
q_spectraTypes = 'av_all',
q_spectraFilter = TRUE,
q_pol = NA,
l_xcmsGroups = c(12, 27),
l_spectraTypes = 'av_all',
l_pol = NA,
l_spectraFilter = TRUE,
cores=1,
updateDb = TRUE,
copyDb = TRUE,
usePrecursors=TRUE,
outPth = sm_out_pth)
matched <- result$matchedResults
expect_equal(matched$lpid, c(1666, 1670))
expect_equal(matched$qpid, c(1666, 1670))
expect_equal(matched$dpc, c(1,1))
expect_equal(matched$rdpc, c(1,1))
expect_equal(matched$cdpc, c(1,1))
expect_equal(matched$mcount, c(3, 1))
expect_equal(matched$allcount, c(3, 1))
xcmsMatchedResults <- result$xcmsMatchedResults
expect_equal(xcmsMatchedResults$pid, c(1666, 1670))
expect_equal(xcmsMatchedResults$lpid, c(1666, 1670))
expect_equal(xcmsMatchedResults$grpid, c(12, 27))
})
test_that("checking spectral matching functions (spectralMatching) query(scans) vs library", {
print ("\n")
print("#################################################################")
print("## Testing spectral matching (spectralMatching) q(scan) v q ##")
print("#################################################################")
td <- tempdir()
q_dbPth <- system.file("extdata", "tests", "db", "createDatabase_example.sqlite", package="msPurity")
rid <- paste0(paste0(sample(LETTERS, 5, TRUE), collapse=""), paste0(sample(9999, 1, TRUE), collapse=""), ".sqlite")
sm_out_pth <- file.path(td, rid)
result <- spectralMatching(q_dbPth, q_xcmsGroups = c(12, 27), cores=1, l_accessions=c('CCMSLIB00000577898','CE000616'),
q_spectraTypes = 'scan',
updateDb = TRUE,
copyDb = TRUE,
outPth = sm_out_pth)
matched <- result$matchedResults
expect_equal(matched$lpid, c(5325, 5325, 5325, 5325, 5325, 5325, 53807, 53807, 53807, 53807, 53807, 53807))
expect_equal(matched$qpid, c(226, 281, 336, 1110, 1166, 1055, 509, 394, 451, 1220, 1275, 1330))
expect_equal(round(matched$dpc,2), c(0.14, 0.03, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0))
expect_equal(round(matched$rdpc,2), c( 0.87 , 0.87 ,NaN ,NaN ,NaN ,NaN ,NaN ,NaN ,NaN ,NaN ,NaN ,NaN ))
expect_equal(round(matched$cdpc,2), c(0.13, 0.03, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0))
expect_equal(matched$mcount, c(1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0))
expect_equal(matched$allcount, c(34, 46, 56, 53, 37, 43, 34, 59, 30, 24, 40, 29))
xcmsMatchedResults <- result$xcmsMatchedResults
expect_equal(xcmsMatchedResults$grpid, c(12, 12, 12, 12, 12, 12, 27, 27, 27, 27, 27, 27))
})
Try the msPurity package in your browser
Any scripts or data that you put into this service are public.
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.