tests/testthat/test.2_purityA_OLD.R
In Viant-Metabolomics/msPurity: Automated Evaluation of Precursor Ion Purity for Mass Spectrometry Based Fragmentation in Metabolomics
context ("checking purityA (using the XCMS v2 functions)")
test_that("checking frag4feature (xcms v2 functions)", {
print("\n")
print("########################################################")
print("## Checking frag4feature (xcms v2 functions) ##")
print("########################################################")
#msmsPths <- list.files(system.file("extdata", "lcms", "mzML", package="msPurityData"), full.names = TRUE, pattern = "MSMS")
#pa <- purityA(msmsPths)
#xset <- xcmsSet(msmsPths)
#xset <- group(xset)
msmsPths <- list.files(system.file("extdata", "lcms", "mzML", package="msPurityData"), full.names = TRUE, pattern = "MSMS")
pa <- readRDS(system.file("extdata", "tests", "purityA", "1_purityA_pa_OLD.rds", package="msPurity"))
xset <- readRDS(system.file("extdata","tests", "xcms", "msms_only_xset_OLD.rds", package="msPurity"))
pa@fileList[1] <- msmsPths[basename(msmsPths)=="LCMSMS_1.mzML"]
pa@fileList[2] <- msmsPths[basename(msmsPths)=="LCMSMS_2.mzML"]
xset@filepaths[1] <- msmsPths[basename(msmsPths)=="LCMSMS_1.mzML"]
xset@filepaths[2] <- msmsPths[basename(msmsPths)=="LCMSMS_2.mzML"]
pa <- frag4feature(pa, xset, create_db=FALSE)
#saveRDS(pa, file.path("inst", "extdata", "test_data", "purityA", "2_frag4feature_pa.rds"))
expect_equal(round(pa@grped_df$inPurity[1],4), 1)
expect_equal(round(pa@grped_df$precurMtchPPM[1], 4), 1.0048)
expect_equal(length(pa@grped_ms2), 77)
expect_equal(nrow(pa@grped_ms2[[2]][[1]]), 4)
expect_equal(round(pa@grped_ms2[[1]][[1]][1],4), 112.0509)
pa_saved <- readRDS(system.file("extdata", "tests", "purityA", "2_frag4feature_pa.rds", package="msPurity"))
# Saved object is from an old version of msPurity where we stored the rtminCorrected differently (no correction used here
# so not important to check for this test)
grped_df <- pa@grped_df[,-match(c('rtminCorrected', 'rtmaxCorrected'), colnames(pa@grped_df))]
grped_df_saved <- pa@grped_df[,-match(c('rtminCorrected', 'rtmaxCorrected'), colnames(pa@grped_df))]
expect_equal(grped_df, grped_df_saved)
})
test_that("checking frag4feature (fillpeaks) (xcms v2 functions)", {
print("\n")
print("####################################################################")
print("## Checking frag4feature (fillpeaks) (xcms v2 functions) ##")
print("####################################################################")
library(xcms)
#msmsPths <- list.files(system.file("extdata", "lcms", "mzML", package="msPurityData"), full.names = TRUE, pattern = "MSMS")
#pa <- purityA(msmsPths)
#xset <- xcmsSet(msmsPths)
#xset <- group(xset)
msmsPths <- list.files(system.file("extdata", "lcms", "mzML", package="msPurityData"), full.names = TRUE, pattern = "MSMS")
pa <- readRDS(system.file("extdata", "tests", "purityA", "1_purityA_pa_OLD.rds", package="msPurity"))
xset <- readRDS(system.file("extdata","tests", "xcms", "msms_only_xset_OLD.rds", package="msPurity"))
pa@fileList[1] <- msmsPths[basename(msmsPths)=="LCMSMS_1.mzML"]
pa@fileList[2] <- msmsPths[basename(msmsPths)=="LCMSMS_2.mzML"]
xset@filepaths[1] <- msmsPths[basename(msmsPths)=="LCMSMS_1.mzML"]
xset@filepaths[2] <- msmsPths[basename(msmsPths)=="LCMSMS_2.mzML"]
xset <- xcms::fillPeaks(xset)
pa <- frag4feature(pa, xset)
#saveRDS(pa, file.path("inst", "extdata", "test_data", "purityA", "2_frag4feature_pa.rds"))
expect_equal(round(pa@grped_df$inPurity[1],4), 1)
expect_equal(round(pa@grped_df$precurMtchPPM[1], 4), 1.0048)
expect_equal(length(pa@grped_ms2), 77)
expect_equal(nrow(pa@grped_ms2[[2]][[1]]), 4)
expect_equal(round(pa@grped_ms2[[1]][[1]][1],4), 112.0509)
pa_saved <- readRDS(system.file("extdata", "tests", "purityA", "2_frag4feature_pa_OLD.rds", package="msPurity"))
if (length(colnames(pa@grped_ms2[[1]][[1]]))>0){
# From R v4.2 onwards XCMS has changed to labelling MS2 spectra - so we add these labels to the saved pa object
grped_ms2_labelled <- lapply(pa_saved@grped_ms2, function(x){
lapply(x, function(y){colnames(y) = c('mz', 'intensity'); return(y)})
})
expect_equal(pa@grped_ms2[1:32], grped_ms2_labelled[1:32])
}else{
expect_equal(pa@grped_ms2, pa@grped_ms2)
}
# Saved object is from an old version of msPurity where we stored the rtminCorrected differently (no correction used here
# so not important to check for this test)
grped_df <- pa@grped_df[,-match(c('rtminCorrected', 'rtmaxCorrected'), colnames(pa@grped_df))]
grped_df_saved <- pa@grped_df[,-match(c('rtminCorrected', 'rtmaxCorrected'), colnames(pa@grped_df))]
expect_equal(grped_df, grped_df_saved)
})
test_that("checking filterFragSpectra purityA (xcms v2 functions)", {
print ("\n")
print("########################################################")
print("## Checking filterFragSpectra (xcms v2 functions) ##")
print("########################################################")
pa <- readRDS(system.file("extdata", "tests", "purityA", "2_frag4feature_pa_OLD.rds", package="msPurity"))
pa <- filterFragSpectra(pa, plim = 0.7, snr = 3)
#saveRDS(pa, file.path("inst", "extdata", "purityA_tests", "3_filterFragSpectra_pa.rds"))
expect_equal(colnames(pa@grped_ms2[[1]][[1]]), c("mz", "i","snr", "ra" ,
"purity_pass_flag", "intensity_pass_flag",
"ra_pass_flag","snr_pass_flag", "pass_flag" ))
expect_equal(round(pa@grped_ms2[[1]][[1]][,'mz'],4), c(112.0509, 126.5377))
expect_equal(round(pa@grped_ms2[[1]][[1]][,'i'],0), c(565117, 2499))
expect_equal(pa@grped_ms2[[1]][[1]][,'snr'], c(1.991193651, 0.008806349))
expect_equal(pa@grped_ms2[[1]][[1]][,'ra'], c(100.0000000, 0.4422648))
expect_equal(pa@grped_ms2[[1]][[1]][,'purity_pass_flag'], c(1, 1))
expect_equal(pa@grped_ms2[[1]][[1]][,'intensity_pass_flag'], c(1, 1))
expect_equal(pa@grped_ms2[[1]][[1]][,'ra_pass_flag'], c(1, 1))
expect_equal(pa@grped_ms2[[1]][[1]][,'snr_pass_flag'], c(0, 0))
expect_equal(pa@grped_ms2[[1]][[1]][,'pass_flag'], c(0, 0))
expect_equal(round(pa@grped_ms2[[10]][[2]][,'mz'],4), c(102.0013, 102.0376, 102.0553, 102.9030,
103.0827, 120.0116, 122.0163, 130.0501,
130.0860, 131.0527, 131.0899, 133.0192,
134.0267, 148.0426, 160.7018))
expect_equal(round(pa@grped_ms2[[10]][[2]][,'i'],0), c( 418361, 26940, 31788, 2297, 2656, 1534089,
2559, 17183, 4825, 3329, 3828,
31002, 3603, 1333086, 2493))
expect_equal(pa@grped_ms2[[10]][[2]][,'snr'], c(86.7093726, 5.5836066, 6.5882984, 0.4761153,
0.5504728, 317.9551029, 0.5304692, 3.5613499,
1.0000000, 0.6899905, 0.7933997, 6.4254739,
0.7467862,276.2951708, 0.5167274))
expect_equal(pa@grped_ms2[[10]][[2]][,'ra'], c( 27.2709486, 1.7560991, 2.0720845, 0.1497429, 0.1731291,
100.0000000, 0.1668378, 1.1200795, 0.3145098, 0.2170088,
0.2495320, 2.0208746, 0.2348716, 86.8975425, 0.1625158))
expect_equal(pa@grped_ms2[[10]][[2]][,'purity_pass_flag'], c( 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1))
expect_equal(pa@grped_ms2[[10]][[2]][,'intensity_pass_flag'], c( 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1))
expect_equal(pa@grped_ms2[[10]][[2]][,'ra_pass_flag'], c( 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1))
expect_equal(pa@grped_ms2[[10]][[2]][,'snr_pass_flag'], c(1, 1, 1, 0, 0, 1, 0, 1, 0, 0 ,0, 1, 0, 1, 0))
expect_equal(pa@grped_ms2[[10]][[2]][,'pass_flag'], c(1, 1, 1, 0, 0, 1, 0, 1, 0, 0 ,0, 1, 0, 1, 0))
pa_saved <- readRDS(system.file("extdata", "tests", "purityA", "3_filterFragSpectra_pa_OLD.rds", package="msPurity"))
expect_equal(pa, pa_saved)
})
test_that("checking averageIntraFragSpectra (no filter) purityA (xcms v2 functions)", {
print ("\n")
print("##############################################################")
print("## Checking averageIntraFragSpectra (xcms v2 functions) ##")
print("##############################################################")
pa <- readRDS(system.file("extdata", "tests", "purityA", "2_frag4feature_pa_OLD.rds", package="msPurity"))
pa <- averageIntraFragSpectra(pa)
#saveRDS(pa, file.path("inst", "extdata", "test_data", "purityA", "4_averageIntraFragSpectra_no_filter_pa.rds"))
expect_equal(length(pa@av_spectra), 77)
expect_equal(length(pa@av_spectra$`12`$av_intra), 2)
expect_equal(round(pa@av_spectra$`12`$av_intra$`1`$mz, 4), c(107.2701, 116.0165, 116.0709, 116.1073))
expect_equal(round(pa@av_spectra$`12`$av_intra$`2`$mz, 4), c(103.1290, 116.0168, 116.0709, 116.1073, 130.0276))
expect_equal(round(pa@av_spectra$`12`$av_intra$`1`$frac, 4), c(0.3333, 0.6667, 1.0000, 0.6667))
expect_equal(round(pa@av_spectra$`12`$av_intra$`2`$frac, 4), c(0.3333, 1.0000, 1.0000, 0.6667, 0.3333))
expect_equal(round(pa@av_spectra$`12`$av_intra$`1`$i, 2), c(1726.61, 7324.86, 2114202.40, 13797.10))
expect_equal(round(pa@av_spectra$`12`$av_intra$`2`$i, 2), c( 4419.71, 23772.87, 2029273.85, 12305.23, 4081.14))
pa_saved <- readRDS(system.file("extdata","tests", "purityA", "4_averageIntraFragSpectra_no_filter_pa_OLD.rds", package="msPurity"))
expect_equal(pa, pa_saved)
})
test_that("checking averageInterFragSpectra (no filter) purityA (xcms v2 functions)", {
print ("\n")
print("#############################################################")
print("## Checking averageInterFragSpectra (xcms v2 functions) #")
print("#############################################################")
pa <- readRDS(system.file("extdata", "tests", "purityA", "4_averageIntraFragSpectra_no_filter_pa_OLD.rds", package="msPurity"))
pa <- averageInterFragSpectra(pa)
#saveRDS(pa, file.path("inst", "extdata", "purityA_tests", "5_averageInterFragSpectra_no_filter_pa.rds"))
expect_equal(length(pa@av_spectra$`12`$av_inter), 15)
expect_equal(round(pa@av_spectra$`12`$av_inter$mz, 4), c(116.0166,116.0709,116.1073))
expect_equal(round(pa@av_spectra$`12`$av_inter$frac, 4), c(1,1,1))
expect_equal(round(pa@av_spectra$`12`$av_inter$i, 2), c(31097.73, 4143476.25, 26102.33))
pa_saved <- readRDS(system.file("extdata","tests", "purityA", "5_averageInterFragSpectra_no_filter_pa_OLD.rds", package="msPurity"))
expect_equal(pa, pa_saved)
})
test_that("checking averageAllFragSpectra (no filter) purityA", {
print ("\n")
print("########################################################")
print("## Checking averageAllFragSpectra (xcms v2 functions) #")
print("########################################################")
pa <- readRDS(system.file("extdata", "tests", "purityA", "5_averageInterFragSpectra_no_filter_pa_OLD.rds", package="msPurity"))
pa <- averageAllFragSpectra(pa)
#saveRDS(pa, file.path("inst", "extdata", "tests", "purityA", "6_averageAllFragSpectra_no_filter_pa.rds"))
expect_equal(length(pa@av_spectra$`12`$av_all), 15)
expect_equal(round(pa@av_spectra$`12`$av_all$mz, 4), c(103.1290, 107.2701, 116.0166, 116.0709, 116.1073, 130.0276))
expect_equal(round(pa@av_spectra$`12`$av_all$frac, 4), c(0.1667, 0.1667, 0.8333, 1.0000, 0.6667, 0.1667))
expect_equal(round(pa@av_spectra$`12`$av_all$i, 2), c(4419.71, 1726.61, 31097.73, 4143476.25, 26102.33, 4081.14))
expect_equal(round(pa@av_spectra$`12`$av_all$mz, 4), c(103.1290, 107.2701, 116.0166, 116.0709, 116.1073, 130.0276))
expect_equal(round(pa@av_spectra$`12`$av_all$frac, 4), c(0.1667, 0.1667, 0.8333, 1.0000, 0.6667, 0.1667))
expect_equal(round(pa@av_spectra$`12`$av_all$i, 2), c(4419.71, 1726.61, 31097.73, 4143476.25, 26102.33, 4081.14))
pa_saved <- readRDS(system.file("extdata", "tests", "purityA", "6_averageAllFragSpectra_no_filter_pa_OLD.rds", package="msPurity"))
expect_equal(pa, pa_saved)
})
test_that("checking averageIntraFragSpectra (with filter) purityA (xcms v2 functions)", {
print ("\n")
print("###########################################################################")
print("## Checking averageIntraFragSpectra (with filter) (xcms v2 functions) ##")
print("###########################################################################")
pa <- readRDS(system.file("extdata", "tests", "purityA", "3_filterFragSpectra_pa_OLD.rds", package="msPurity"))
pa <- averageIntraFragSpectra(pa)
#saveRDS(pa, file.path("inst", "extdata", "tests", "purityA", "7_averageIntraFragSpectra_with_filter_pa.rds"))
pa_saved <- readRDS(system.file("extdata","tests", "purityA", "7_averageIntraFragSpectra_with_filter_pa_OLD.rds", package="msPurity"))
expect_equal(pa, pa_saved)
})
test_that("checking averageInterFragSpectra (with filter) purityA (xcms v2 functions)", {
print ("\n")
print("############################################################################")
print("## Checking averageInterFragSpectra (with filter) (xcms v2 functions) ##")
print("############################################################################")
pa <- readRDS(system.file("extdata", "tests", "purityA", "7_averageIntraFragSpectra_with_filter_pa_OLD.rds", package="msPurity"))
pa <- averageInterFragSpectra(pa)
#saveRDS(pa, file.path("inst", "extdata", "tests", "purityA", "8_averageInterFragSpectra_with_filter_pa.rds"))
pa_saved <- readRDS(system.file("extdata","tests", "purityA", "8_averageInterFragSpectra_with_filter_pa_OLD.rds", package="msPurity"))
expect_equal(pa, pa_saved)
})
test_that("checking averageAllFragSpectra (with filter) purityA (xcms v2 functions)", {
print ("\n")
print("#########################################################################")
print("## Checking averageAllFragSpectra (with filter) (xcms v2 functions) ##")
print("#########################################################################")
pa <- readRDS(system.file("extdata", "tests", "purityA", "8_averageInterFragSpectra_with_filter_pa_OLD.rds", package="msPurity"))
pa <- averageAllFragSpectra(pa)
#saveRDS(pa, file.path("inst", "extdata", "tests", "purityA", "9_averageAllFragSpectra_with_filter_pa.rds"))
pa_saved <- readRDS(system.file("extdata", "tests", "purityA", "9_averageAllFragSpectra_with_filter_pa_OLD.rds", package="msPurity"))
expect_equal(pa, pa_saved)
})
test_that("checking createMSP based functions (xcms v2 functions)", {
print ("\n")
print("########################################################")
print("## Checking createMSP functions (xcms v2 functions) ##")
print("########################################################")
pa <- readRDS(system.file("extdata", "tests", "purityA", "9_averageAllFragSpectra_with_filter_pa_OLD.rds", package="msPurity"))
get_msp_str <- function(msp_pth){
msp_str <- readChar(msp_pth, file.info(msp_pth)$size)
msp_str <- gsub('\n','',msp_str)
msp_str <- gsub('\r','',msp_str)
msp_str <- gsub('msPurity version:\\d+\\.\\d+\\.\\d+','', msp_str)
return(msp_str)
}
metadata <- data.frame('grpid'=c(12, 27), 'MS$FOCUSED_ION: PRECURSOR_TYPE'=c('[M+H]+', '[M+H]+ 88.0158 [M+H+NH3]+ 105.042'),
'AC$MASS_SPECTROMETRY: ION_MODE'=c("POSITIVE","POSITIVE"), 'CH$NAME:'=c('Sulfamethizole', 'Unknown'),
check.names = FALSE, stringsAsFactors = FALSE)
tmp_dir <- tempdir()
################################
# Check all method
################################
all_msp_new_pth <- file.path(tmp_dir,'all.msp')
createMSP(pa, msp_file = all_msp_new_pth, metadata = metadata,
method = "all", xcms_groupids = c(12, 27))
all_msp_new <- get_msp_str(all_msp_new_pth)
all_msp_old <- get_msp_str(system.file("extdata", "tests", "msp", "all_OLD.msp", package="msPurity"))
expect_equal(all_msp_new, all_msp_old)
################################
# Check max method
################################
max_msp_new_pth <- file.path(tmp_dir,'max.msp')
createMSP(pa, msp_file = max_msp_new_pth, metadata = metadata, method = "max",
xcms_groupids = c(12, 27), filter=FALSE)
max_msp_new <- get_msp_str(max_msp_new_pth)
max_msp_old <- get_msp_str(system.file("extdata", "tests","msp", "max_OLD.msp", package="msPurity"))
expect_equal(max_msp_new, max_msp_old)
################################
# Check av_inter method
################################
av_inter_msp_new_pth <- file.path(tmp_dir,'av_inter.msp')
createMSP(pa, msp_file = av_inter_msp_new_pth, metadata = metadata, method = "av_inter", xcms_groupids = c(12, 27))
av_inter_msp_new <- get_msp_str(av_inter_msp_new_pth)
av_inter_msp_old <- get_msp_str(system.file("extdata","tests","msp", "av_inter_OLD.msp", package="msPurity"))
expect_equal(av_inter_msp_new, av_inter_msp_old)
################################
# Check av_intra method
################################
av_intra_msp_new_pth <- file.path(tmp_dir,'av_intra.msp')
createMSP(pa, msp_file = av_intra_msp_new_pth, metadata = metadata, method = "av_intra", xcms_groupids = c(12, 27))
av_intra_msp_new <- get_msp_str(av_intra_msp_new_pth)
av_intra_msp_old <- get_msp_str(system.file("extdata","tests","msp", "av_intra_OLD.msp", package="msPurity"))
expect_equal(av_intra_msp_new, av_intra_msp_old)
################################
# Check av_all method
################################
av_all_msp_new_pth <- file.path(tmp_dir,'av_all.msp')
createMSP(pa, msp_file = av_all_msp_new_pth, metadata = metadata, method = "av_all", xcms_groupids = c(8, 12))
av_all_msp_new <- get_msp_str(av_all_msp_new_pth)
av_all_msp_old <- get_msp_str(system.file("extdata", "tests","msp", "av_all_OLD.msp", package="msPurity"))
expect_equal(av_all_msp_new, av_all_msp_old)
################################
# When two metadata details for single XCMS feature
################################
metadatad <- metadata
metadatad[3, ] <- metadatad[1,]
metadatad[3,4] <- 'possible other compound'
av_all_msp_new_dupmeta_pth <- file.path(tmp_dir,'av_all_dupmeta.msp')
createMSP(pa, msp_file = av_all_msp_new_dupmeta_pth, metadata = metadatad, method = "av_all", xcms_groupids = c(8, 12))
av_all_msp_dupmeta_new <- get_msp_str(av_all_msp_new_dupmeta_pth)
av_all_msp_dupmeta_old <- get_msp_str(system.file("extdata", "tests","msp", "av_all_dupmeta_OLD.msp", package="msPurity"))
expect_equal(av_all_msp_dupmeta_new, av_all_msp_dupmeta_old)
################################
# When the RECORD_TITLE: is defined by user
################################
metadata <- data.frame('grpid'=c(12, 27), 'MS$FOCUSED_ION: PRECURSOR_TYPE'=c('[M+H]+', '[M+H]+ 88.0158 [M+H+NH3]+ 105.042'),
'AC$MASS_SPECTROMETRY: ION_MODE'=c("POSITIVE","POSITIVE"), 'RECORD_TITLE:'=c('Sulfamethizole', 'Unknown'),
check.names = FALSE, stringsAsFactors = FALSE)
recrdt_msp_new_pth <- file.path(tmp_dir,'recrdt.msp')
createMSP(pa, msp_file = recrdt_msp_new_pth, metadata = metadata,
method = "all", xcms_groupids = c(12, 27))
recrdt_msp_new <- get_msp_str(recrdt_msp_new_pth)
recrdt_msp_old <- get_msp_str(system.file("extdata", "tests", "msp", "recrdt_OLD.msp", package="msPurity"))
expect_equal(recrdt_msp_new, recrdt_msp_old)
})
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context ("checking purityA (using the XCMS v2 functions)")
test_that("checking frag4feature (xcms v2 functions)", {
print("\n")
print("########################################################")
print("## Checking frag4feature (xcms v2 functions) ##")
print("########################################################")
#msmsPths <- list.files(system.file("extdata", "lcms", "mzML", package="msPurityData"), full.names = TRUE, pattern = "MSMS")
#pa <- purityA(msmsPths)
#xset <- xcmsSet(msmsPths)
#xset <- group(xset)
msmsPths <- list.files(system.file("extdata", "lcms", "mzML", package="msPurityData"), full.names = TRUE, pattern = "MSMS")
pa <- readRDS(system.file("extdata", "tests", "purityA", "1_purityA_pa_OLD.rds", package="msPurity"))
xset <- readRDS(system.file("extdata","tests", "xcms", "msms_only_xset_OLD.rds", package="msPurity"))
pa@fileList[1] <- msmsPths[basename(msmsPths)=="LCMSMS_1.mzML"]
pa@fileList[2] <- msmsPths[basename(msmsPths)=="LCMSMS_2.mzML"]
xset@filepaths[1] <- msmsPths[basename(msmsPths)=="LCMSMS_1.mzML"]
xset@filepaths[2] <- msmsPths[basename(msmsPths)=="LCMSMS_2.mzML"]
pa <- frag4feature(pa, xset, create_db=FALSE)
#saveRDS(pa, file.path("inst", "extdata", "test_data", "purityA", "2_frag4feature_pa.rds"))
expect_equal(round(pa@grped_df$inPurity[1],4), 1)
expect_equal(round(pa@grped_df$precurMtchPPM[1], 4), 1.0048)
expect_equal(length(pa@grped_ms2), 77)
expect_equal(nrow(pa@grped_ms2[[2]][[1]]), 4)
expect_equal(round(pa@grped_ms2[[1]][[1]][1],4), 112.0509)
pa_saved <- readRDS(system.file("extdata", "tests", "purityA", "2_frag4feature_pa.rds", package="msPurity"))
# Saved object is from an old version of msPurity where we stored the rtminCorrected differently (no correction used here
# so not important to check for this test)
grped_df <- pa@grped_df[,-match(c('rtminCorrected', 'rtmaxCorrected'), colnames(pa@grped_df))]
grped_df_saved <- pa@grped_df[,-match(c('rtminCorrected', 'rtmaxCorrected'), colnames(pa@grped_df))]
expect_equal(grped_df, grped_df_saved)
})
test_that("checking frag4feature (fillpeaks) (xcms v2 functions)", {
print("\n")
print("####################################################################")
print("## Checking frag4feature (fillpeaks) (xcms v2 functions) ##")
print("####################################################################")
library(xcms)
#msmsPths <- list.files(system.file("extdata", "lcms", "mzML", package="msPurityData"), full.names = TRUE, pattern = "MSMS")
#pa <- purityA(msmsPths)
#xset <- xcmsSet(msmsPths)
#xset <- group(xset)
msmsPths <- list.files(system.file("extdata", "lcms", "mzML", package="msPurityData"), full.names = TRUE, pattern = "MSMS")
pa <- readRDS(system.file("extdata", "tests", "purityA", "1_purityA_pa_OLD.rds", package="msPurity"))
xset <- readRDS(system.file("extdata","tests", "xcms", "msms_only_xset_OLD.rds", package="msPurity"))
pa@fileList[1] <- msmsPths[basename(msmsPths)=="LCMSMS_1.mzML"]
pa@fileList[2] <- msmsPths[basename(msmsPths)=="LCMSMS_2.mzML"]
xset@filepaths[1] <- msmsPths[basename(msmsPths)=="LCMSMS_1.mzML"]
xset@filepaths[2] <- msmsPths[basename(msmsPths)=="LCMSMS_2.mzML"]
xset <- xcms::fillPeaks(xset)
pa <- frag4feature(pa, xset)
#saveRDS(pa, file.path("inst", "extdata", "test_data", "purityA", "2_frag4feature_pa.rds"))
expect_equal(round(pa@grped_df$inPurity[1],4), 1)
expect_equal(round(pa@grped_df$precurMtchPPM[1], 4), 1.0048)
expect_equal(length(pa@grped_ms2), 77)
expect_equal(nrow(pa@grped_ms2[[2]][[1]]), 4)
expect_equal(round(pa@grped_ms2[[1]][[1]][1],4), 112.0509)
pa_saved <- readRDS(system.file("extdata", "tests", "purityA", "2_frag4feature_pa_OLD.rds", package="msPurity"))
if (length(colnames(pa@grped_ms2[[1]][[1]]))>0){
# From R v4.2 onwards XCMS has changed to labelling MS2 spectra - so we add these labels to the saved pa object
grped_ms2_labelled <- lapply(pa_saved@grped_ms2, function(x){
lapply(x, function(y){colnames(y) = c('mz', 'intensity'); return(y)})
})
expect_equal(pa@grped_ms2[1:32], grped_ms2_labelled[1:32])
}else{
expect_equal(pa@grped_ms2, pa@grped_ms2)
}
# Saved object is from an old version of msPurity where we stored the rtminCorrected differently (no correction used here
# so not important to check for this test)
grped_df <- pa@grped_df[,-match(c('rtminCorrected', 'rtmaxCorrected'), colnames(pa@grped_df))]
grped_df_saved <- pa@grped_df[,-match(c('rtminCorrected', 'rtmaxCorrected'), colnames(pa@grped_df))]
expect_equal(grped_df, grped_df_saved)
})
test_that("checking filterFragSpectra purityA (xcms v2 functions)", {
print ("\n")
print("########################################################")
print("## Checking filterFragSpectra (xcms v2 functions) ##")
print("########################################################")
pa <- readRDS(system.file("extdata", "tests", "purityA", "2_frag4feature_pa_OLD.rds", package="msPurity"))
pa <- filterFragSpectra(pa, plim = 0.7, snr = 3)
#saveRDS(pa, file.path("inst", "extdata", "purityA_tests", "3_filterFragSpectra_pa.rds"))
expect_equal(colnames(pa@grped_ms2[[1]][[1]]), c("mz", "i","snr", "ra" ,
"purity_pass_flag", "intensity_pass_flag",
"ra_pass_flag","snr_pass_flag", "pass_flag" ))
expect_equal(round(pa@grped_ms2[[1]][[1]][,'mz'],4), c(112.0509, 126.5377))
expect_equal(round(pa@grped_ms2[[1]][[1]][,'i'],0), c(565117, 2499))
expect_equal(pa@grped_ms2[[1]][[1]][,'snr'], c(1.991193651, 0.008806349))
expect_equal(pa@grped_ms2[[1]][[1]][,'ra'], c(100.0000000, 0.4422648))
expect_equal(pa@grped_ms2[[1]][[1]][,'purity_pass_flag'], c(1, 1))
expect_equal(pa@grped_ms2[[1]][[1]][,'intensity_pass_flag'], c(1, 1))
expect_equal(pa@grped_ms2[[1]][[1]][,'ra_pass_flag'], c(1, 1))
expect_equal(pa@grped_ms2[[1]][[1]][,'snr_pass_flag'], c(0, 0))
expect_equal(pa@grped_ms2[[1]][[1]][,'pass_flag'], c(0, 0))
expect_equal(round(pa@grped_ms2[[10]][[2]][,'mz'],4), c(102.0013, 102.0376, 102.0553, 102.9030,
103.0827, 120.0116, 122.0163, 130.0501,
130.0860, 131.0527, 131.0899, 133.0192,
134.0267, 148.0426, 160.7018))
expect_equal(round(pa@grped_ms2[[10]][[2]][,'i'],0), c( 418361, 26940, 31788, 2297, 2656, 1534089,
2559, 17183, 4825, 3329, 3828,
31002, 3603, 1333086, 2493))
expect_equal(pa@grped_ms2[[10]][[2]][,'snr'], c(86.7093726, 5.5836066, 6.5882984, 0.4761153,
0.5504728, 317.9551029, 0.5304692, 3.5613499,
1.0000000, 0.6899905, 0.7933997, 6.4254739,
0.7467862,276.2951708, 0.5167274))
expect_equal(pa@grped_ms2[[10]][[2]][,'ra'], c( 27.2709486, 1.7560991, 2.0720845, 0.1497429, 0.1731291,
100.0000000, 0.1668378, 1.1200795, 0.3145098, 0.2170088,
0.2495320, 2.0208746, 0.2348716, 86.8975425, 0.1625158))
expect_equal(pa@grped_ms2[[10]][[2]][,'purity_pass_flag'], c( 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1))
expect_equal(pa@grped_ms2[[10]][[2]][,'intensity_pass_flag'], c( 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1))
expect_equal(pa@grped_ms2[[10]][[2]][,'ra_pass_flag'], c( 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1))
expect_equal(pa@grped_ms2[[10]][[2]][,'snr_pass_flag'], c(1, 1, 1, 0, 0, 1, 0, 1, 0, 0 ,0, 1, 0, 1, 0))
expect_equal(pa@grped_ms2[[10]][[2]][,'pass_flag'], c(1, 1, 1, 0, 0, 1, 0, 1, 0, 0 ,0, 1, 0, 1, 0))
pa_saved <- readRDS(system.file("extdata", "tests", "purityA", "3_filterFragSpectra_pa_OLD.rds", package="msPurity"))
expect_equal(pa, pa_saved)
})
test_that("checking averageIntraFragSpectra (no filter) purityA (xcms v2 functions)", {
print ("\n")
print("##############################################################")
print("## Checking averageIntraFragSpectra (xcms v2 functions) ##")
print("##############################################################")
pa <- readRDS(system.file("extdata", "tests", "purityA", "2_frag4feature_pa_OLD.rds", package="msPurity"))
pa <- averageIntraFragSpectra(pa)
#saveRDS(pa, file.path("inst", "extdata", "test_data", "purityA", "4_averageIntraFragSpectra_no_filter_pa.rds"))
expect_equal(length(pa@av_spectra), 77)
expect_equal(length(pa@av_spectra$`12`$av_intra), 2)
expect_equal(round(pa@av_spectra$`12`$av_intra$`1`$mz, 4), c(107.2701, 116.0165, 116.0709, 116.1073))
expect_equal(round(pa@av_spectra$`12`$av_intra$`2`$mz, 4), c(103.1290, 116.0168, 116.0709, 116.1073, 130.0276))
expect_equal(round(pa@av_spectra$`12`$av_intra$`1`$frac, 4), c(0.3333, 0.6667, 1.0000, 0.6667))
expect_equal(round(pa@av_spectra$`12`$av_intra$`2`$frac, 4), c(0.3333, 1.0000, 1.0000, 0.6667, 0.3333))
expect_equal(round(pa@av_spectra$`12`$av_intra$`1`$i, 2), c(1726.61, 7324.86, 2114202.40, 13797.10))
expect_equal(round(pa@av_spectra$`12`$av_intra$`2`$i, 2), c( 4419.71, 23772.87, 2029273.85, 12305.23, 4081.14))
pa_saved <- readRDS(system.file("extdata","tests", "purityA", "4_averageIntraFragSpectra_no_filter_pa_OLD.rds", package="msPurity"))
expect_equal(pa, pa_saved)
})
test_that("checking averageInterFragSpectra (no filter) purityA (xcms v2 functions)", {
print ("\n")
print("#############################################################")
print("## Checking averageInterFragSpectra (xcms v2 functions) #")
print("#############################################################")
pa <- readRDS(system.file("extdata", "tests", "purityA", "4_averageIntraFragSpectra_no_filter_pa_OLD.rds", package="msPurity"))
pa <- averageInterFragSpectra(pa)
#saveRDS(pa, file.path("inst", "extdata", "purityA_tests", "5_averageInterFragSpectra_no_filter_pa.rds"))
expect_equal(length(pa@av_spectra$`12`$av_inter), 15)
expect_equal(round(pa@av_spectra$`12`$av_inter$mz, 4), c(116.0166,116.0709,116.1073))
expect_equal(round(pa@av_spectra$`12`$av_inter$frac, 4), c(1,1,1))
expect_equal(round(pa@av_spectra$`12`$av_inter$i, 2), c(31097.73, 4143476.25, 26102.33))
pa_saved <- readRDS(system.file("extdata","tests", "purityA", "5_averageInterFragSpectra_no_filter_pa_OLD.rds", package="msPurity"))
expect_equal(pa, pa_saved)
})
test_that("checking averageAllFragSpectra (no filter) purityA", {
print ("\n")
print("########################################################")
print("## Checking averageAllFragSpectra (xcms v2 functions) #")
print("########################################################")
pa <- readRDS(system.file("extdata", "tests", "purityA", "5_averageInterFragSpectra_no_filter_pa_OLD.rds", package="msPurity"))
pa <- averageAllFragSpectra(pa)
#saveRDS(pa, file.path("inst", "extdata", "tests", "purityA", "6_averageAllFragSpectra_no_filter_pa.rds"))
expect_equal(length(pa@av_spectra$`12`$av_all), 15)
expect_equal(round(pa@av_spectra$`12`$av_all$mz, 4), c(103.1290, 107.2701, 116.0166, 116.0709, 116.1073, 130.0276))
expect_equal(round(pa@av_spectra$`12`$av_all$frac, 4), c(0.1667, 0.1667, 0.8333, 1.0000, 0.6667, 0.1667))
expect_equal(round(pa@av_spectra$`12`$av_all$i, 2), c(4419.71, 1726.61, 31097.73, 4143476.25, 26102.33, 4081.14))
expect_equal(round(pa@av_spectra$`12`$av_all$mz, 4), c(103.1290, 107.2701, 116.0166, 116.0709, 116.1073, 130.0276))
expect_equal(round(pa@av_spectra$`12`$av_all$frac, 4), c(0.1667, 0.1667, 0.8333, 1.0000, 0.6667, 0.1667))
expect_equal(round(pa@av_spectra$`12`$av_all$i, 2), c(4419.71, 1726.61, 31097.73, 4143476.25, 26102.33, 4081.14))
pa_saved <- readRDS(system.file("extdata", "tests", "purityA", "6_averageAllFragSpectra_no_filter_pa_OLD.rds", package="msPurity"))
expect_equal(pa, pa_saved)
})
test_that("checking averageIntraFragSpectra (with filter) purityA (xcms v2 functions)", {
print ("\n")
print("###########################################################################")
print("## Checking averageIntraFragSpectra (with filter) (xcms v2 functions) ##")
print("###########################################################################")
pa <- readRDS(system.file("extdata", "tests", "purityA", "3_filterFragSpectra_pa_OLD.rds", package="msPurity"))
pa <- averageIntraFragSpectra(pa)
#saveRDS(pa, file.path("inst", "extdata", "tests", "purityA", "7_averageIntraFragSpectra_with_filter_pa.rds"))
pa_saved <- readRDS(system.file("extdata","tests", "purityA", "7_averageIntraFragSpectra_with_filter_pa_OLD.rds", package="msPurity"))
expect_equal(pa, pa_saved)
})
test_that("checking averageInterFragSpectra (with filter) purityA (xcms v2 functions)", {
print ("\n")
print("############################################################################")
print("## Checking averageInterFragSpectra (with filter) (xcms v2 functions) ##")
print("############################################################################")
pa <- readRDS(system.file("extdata", "tests", "purityA", "7_averageIntraFragSpectra_with_filter_pa_OLD.rds", package="msPurity"))
pa <- averageInterFragSpectra(pa)
#saveRDS(pa, file.path("inst", "extdata", "tests", "purityA", "8_averageInterFragSpectra_with_filter_pa.rds"))
pa_saved <- readRDS(system.file("extdata","tests", "purityA", "8_averageInterFragSpectra_with_filter_pa_OLD.rds", package="msPurity"))
expect_equal(pa, pa_saved)
})
test_that("checking averageAllFragSpectra (with filter) purityA (xcms v2 functions)", {
print ("\n")
print("#########################################################################")
print("## Checking averageAllFragSpectra (with filter) (xcms v2 functions) ##")
print("#########################################################################")
pa <- readRDS(system.file("extdata", "tests", "purityA", "8_averageInterFragSpectra_with_filter_pa_OLD.rds", package="msPurity"))
pa <- averageAllFragSpectra(pa)
#saveRDS(pa, file.path("inst", "extdata", "tests", "purityA", "9_averageAllFragSpectra_with_filter_pa.rds"))
pa_saved <- readRDS(system.file("extdata", "tests", "purityA", "9_averageAllFragSpectra_with_filter_pa_OLD.rds", package="msPurity"))
expect_equal(pa, pa_saved)
})
test_that("checking createMSP based functions (xcms v2 functions)", {
print ("\n")
print("########################################################")
print("## Checking createMSP functions (xcms v2 functions) ##")
print("########################################################")
pa <- readRDS(system.file("extdata", "tests", "purityA", "9_averageAllFragSpectra_with_filter_pa_OLD.rds", package="msPurity"))
get_msp_str <- function(msp_pth){
msp_str <- readChar(msp_pth, file.info(msp_pth)$size)
msp_str <- gsub('\n','',msp_str)
msp_str <- gsub('\r','',msp_str)
msp_str <- gsub('msPurity version:\\d+\\.\\d+\\.\\d+','', msp_str)
return(msp_str)
}
metadata <- data.frame('grpid'=c(12, 27), 'MS$FOCUSED_ION: PRECURSOR_TYPE'=c('[M+H]+', '[M+H]+ 88.0158 [M+H+NH3]+ 105.042'),
'AC$MASS_SPECTROMETRY: ION_MODE'=c("POSITIVE","POSITIVE"), 'CH$NAME:'=c('Sulfamethizole', 'Unknown'),
check.names = FALSE, stringsAsFactors = FALSE)
tmp_dir <- tempdir()
################################
# Check all method
################################
all_msp_new_pth <- file.path(tmp_dir,'all.msp')
createMSP(pa, msp_file = all_msp_new_pth, metadata = metadata,
method = "all", xcms_groupids = c(12, 27))
all_msp_new <- get_msp_str(all_msp_new_pth)
all_msp_old <- get_msp_str(system.file("extdata", "tests", "msp", "all_OLD.msp", package="msPurity"))
expect_equal(all_msp_new, all_msp_old)
################################
# Check max method
################################
max_msp_new_pth <- file.path(tmp_dir,'max.msp')
createMSP(pa, msp_file = max_msp_new_pth, metadata = metadata, method = "max",
xcms_groupids = c(12, 27), filter=FALSE)
max_msp_new <- get_msp_str(max_msp_new_pth)
max_msp_old <- get_msp_str(system.file("extdata", "tests","msp", "max_OLD.msp", package="msPurity"))
expect_equal(max_msp_new, max_msp_old)
################################
# Check av_inter method
################################
av_inter_msp_new_pth <- file.path(tmp_dir,'av_inter.msp')
createMSP(pa, msp_file = av_inter_msp_new_pth, metadata = metadata, method = "av_inter", xcms_groupids = c(12, 27))
av_inter_msp_new <- get_msp_str(av_inter_msp_new_pth)
av_inter_msp_old <- get_msp_str(system.file("extdata","tests","msp", "av_inter_OLD.msp", package="msPurity"))
expect_equal(av_inter_msp_new, av_inter_msp_old)
################################
# Check av_intra method
################################
av_intra_msp_new_pth <- file.path(tmp_dir,'av_intra.msp')
createMSP(pa, msp_file = av_intra_msp_new_pth, metadata = metadata, method = "av_intra", xcms_groupids = c(12, 27))
av_intra_msp_new <- get_msp_str(av_intra_msp_new_pth)
av_intra_msp_old <- get_msp_str(system.file("extdata","tests","msp", "av_intra_OLD.msp", package="msPurity"))
expect_equal(av_intra_msp_new, av_intra_msp_old)
################################
# Check av_all method
################################
av_all_msp_new_pth <- file.path(tmp_dir,'av_all.msp')
createMSP(pa, msp_file = av_all_msp_new_pth, metadata = metadata, method = "av_all", xcms_groupids = c(8, 12))
av_all_msp_new <- get_msp_str(av_all_msp_new_pth)
av_all_msp_old <- get_msp_str(system.file("extdata", "tests","msp", "av_all_OLD.msp", package="msPurity"))
expect_equal(av_all_msp_new, av_all_msp_old)
################################
# When two metadata details for single XCMS feature
################################
metadatad <- metadata
metadatad[3, ] <- metadatad[1,]
metadatad[3,4] <- 'possible other compound'
av_all_msp_new_dupmeta_pth <- file.path(tmp_dir,'av_all_dupmeta.msp')
createMSP(pa, msp_file = av_all_msp_new_dupmeta_pth, metadata = metadatad, method = "av_all", xcms_groupids = c(8, 12))
av_all_msp_dupmeta_new <- get_msp_str(av_all_msp_new_dupmeta_pth)
av_all_msp_dupmeta_old <- get_msp_str(system.file("extdata", "tests","msp", "av_all_dupmeta_OLD.msp", package="msPurity"))
expect_equal(av_all_msp_dupmeta_new, av_all_msp_dupmeta_old)
################################
# When the RECORD_TITLE: is defined by user
################################
metadata <- data.frame('grpid'=c(12, 27), 'MS$FOCUSED_ION: PRECURSOR_TYPE'=c('[M+H]+', '[M+H]+ 88.0158 [M+H+NH3]+ 105.042'),
'AC$MASS_SPECTROMETRY: ION_MODE'=c("POSITIVE","POSITIVE"), 'RECORD_TITLE:'=c('Sulfamethizole', 'Unknown'),
check.names = FALSE, stringsAsFactors = FALSE)
recrdt_msp_new_pth <- file.path(tmp_dir,'recrdt.msp')
createMSP(pa, msp_file = recrdt_msp_new_pth, metadata = metadata,
method = "all", xcms_groupids = c(12, 27))
recrdt_msp_new <- get_msp_str(recrdt_msp_new_pth)
recrdt_msp_old <- get_msp_str(system.file("extdata", "tests", "msp", "recrdt_OLD.msp", package="msPurity"))
expect_equal(recrdt_msp_new, recrdt_msp_old)
})
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