tests/testthat/test-qcrms-LCMS.R
In computational-metabolomics/qcrms: Creates quality control output from XCMS output
context("LCMS data")
library(xcms)
library(BiocManager)
if(!requireNamespace("msPurityData", quietly=TRUE)){
BiocManager::install("msPurityData")
}
if(!requireNamespace("faahKO", quietly=TRUE)){
BiocManager::install("faahKO")
}
test_that("createQCreportObject works with XCMS LCMS data outputs", {
require(xcms)
## Get the full path to the CDF files
cdfs <- dir(system.file("cdf", package="faahKO"), full.names=TRUE,
recursive=TRUE)
## Create a phenodata data.frame
meta_data <- data.frame(Sample=sub(basename(cdfs), pattern=".CDF",
replacement="", fixed=TRUE),
sample_group=c(rep("QC", 6), "MSMS",rep("WT", 5)),
remove=c(TRUE, rep(NA, 11)),
stringsAsFactors=FALSE)
rownames(meta_data) <- meta_data$Sample
expect_message(raw_data <- readMSData(files=cdfs,
pdata=new("NAnnotatedDataFrame", meta_data), mode="onDisk"))
cwp <- xcms::CentWaveParam(peakwidth = c(20, 80), noise=5000)
xdata <- xcms::findChromPeaks(raw_data, param=cwp)
xdata <- adjustRtime(xdata, param=ObiwarpParam(binSize=0.6))
xdata <- xcms::groupChromPeaks(xdata,
xcms::PeakDensityParam(sampleGroups=rep("S", 12)))
temp_dir <- tempdir()
write.csv(file=file.path(temp_dir, "qcrms_test_meta_data_file.csv"),
meta_data, row.names=F)
save(file=file.path(temp_dir, "LCMS_xdata.Rdata"), list="xdata")
# Create meta data xlsx file format
require (openxlsx)
wb <- createWorkbook()
addWorksheet (wb,"meta")
writeData (wb,"meta", meta_data, rowNames = F)
saveWorkbook (wb, file.path(temp_dir, "qcrms_meta_data.xlsx"),
overwrite = T)
expect_warning(QCreport <- createQCreportObject(
data_file="LCMS_xdata.Rdata", projectdir=temp_dir,
metaData_file="qcrms_test_meta_data_file.csv", xcms_output="xdata",
classLabel="sample_group", excludeQC="remove", msms_label="MSMS"))
expect_true(file.exists(file.path(temp_dir, "LCMS_xdata.xlsx")))
# Check content of output xlsx file
wb_temp <- openxlsx::loadWorkbook(file.path(temp_dir, "LCMS_xdata.xlsx"))
variableMetaData <- readWorkbook(wb_temp, "variableMetaData")
expect_equal(head (variableMetaData),
structure(list(name = c("M205T2791", "M206T2790", "M207T2719",
"M233T3029", "M241T3686", "M244T2835"),
mz=c(205, 206, 207.100006103516, 233, 241.100006103516,
244.100006103516),
mzmin=c(205, 206, 207.100006103516, 233, 241.100006103516,
244.100006103516),
mzmax=c(205, 206, 207.100006103516, 233, 241.199996948242,
244.100006103516),
rt=c(2791.04516601562, 2790.11202148437, 2718.83251953125,
3029.41455078125, 3686.39326269531, 2834.84826660156),
rtmin=c(2787.63159179688, 2786.41528320312, 2712.60815429688,
3014.683, 3671.52124023438, 2830.10083007812),
rtmax=c(2795.03662109375, 2795.61206054688, 2723.601,
3063.19799804688, 3740.9423828125, 2836.123046875),
npeaks=c(12, 12, 13, 11, 20, 6),
S=c(12, 11, 9, 9, 11, 6)),
row.names=c(NA, 6L), class="data.frame")
)
rm (wb_temp)
expect_equal(QCreport$xcms_output, "xdata")
expect_equal(QCreport$pca_scores_labels, "all")
expect_equal(QCreport$data_file, "LCMS_xdata.Rdata")
expect_equal(QCreport$projectdir, temp_dir)
expect_equal(QCreport$filtering$glog_lambda_filtered, 61043890464.6641)
expect_equal(QCreport$filtering$glog_lambda_filtered_SB, 1338305112712.85)
expect_equivalent(QCreport$filtering$table[c(1, 4), ],
data.frame(
Filter=c("Before filtering", "Features, method=QC, fraction=0.9"),
`Number of features`=c(268, 128),
`Number of samples`=c(11, 11),
Applied=c(TRUE, TRUE),
check.names=FALSE, stringsAsFactors=FALSE)
)
expect_equivalent(QCreport$xset@phenoData[c(1, 4, 9), ],
data.frame(
Sample=c("ko15", "ko19", "wt19"),
sample_group=c("QC", "QC", "WT"),
remove=c(TRUE, NA, NA),
class=c(1, 1, 1),
check.names=FALSE,
stringsAsFactors=FALSE)
)
expect_equivalent(QCreport$xset@peaks[1, ],
c(453.2000122, 453.2000122, 453.2000122, 2509.2795410, 2501.3779297,
2528.2773438, 1007408.9731765, 1007380.8042353, 38152.0000000,
38151.0000000, 1)
)
expect_equivalent(QCreport$xset@groups[13:14, ],
matrix(nrow=2, ncol=8, byrow=TRUE,
c(269.2000122, 269.100006, 269.2000122, 3889.45959, 3859.553467,
3900.083740, 16, 11, 279.0000000, 279.0000000, 279.0000000,
2790.799072, 2751.645508, 2801.754883, 19, 12
)
)
)
expect_equal(QCreport$xset@groupidx[[47]],
c(1405, 2436, 2854, 3896, 4299, 4982, 4990))
expect_equivalent(QCreport$xset@rt$raw[[5]][10:15],
c(2515.462, 2517.027, 2518.592, 2520.157, 2521.722, 2523.287))
expect_equivalent(QCreport$xset@rt$corrected[[5]][10:15],
c(2514.697510, 2516.180908, 2517.664795, 2519.149170, 2520.634277,
2522.120361))
expect_equal(QCreport$xset@.processHistory[[1]]@type, "Peak detection")
expect_equal(QCreport$xset@.processHistory[[1]]@param@ppm, 25)
expect_equal(QCreport$xset@.processHistory[[1]]@param@peakwidth, c(20, 80))
expect_equal(QCreport$xset@.processHistory[[1]]@param@snthresh, 10)
expect_equal(QCreport$xset@.processHistory[[1]]@param@mzdiff, -0.001)
expect_equal(QCreport$peakMatrix[1, 1:3],
c(ko15=1924712.01585714, ko16=1757150.9648, ko18=1714581.77647058))
expect_equal(QCreport$metaData$table,
structure(list(
Sample=c("ko15", "ko16", "ko18", "ko19", "ko21", "ko22",
"wt16", "wt18", "wt19", "wt21", "wt22"),
sample_group=c("Removed", "QC", "QC", "QC", "QC", "QC", "WT", "WT",
"WT", "WT", "WT"),
remove=c(TRUE, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA),
injection_order=1:11, batch=c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L)),
row.names=c(1L, 2L, 3L, 4L, 5L, 6L, 8L, 9L, 10L, 11L, 12L),
class="data.frame")
)
expect_equal(QCreport$pca_scores_labels, "all")
expect_equal(QCreport$metaData$classColumn, "sample_group")
# Plots
expect_equal(QCreport$plots$ticplot_1$data[3,1], 754424703.6)
expect_equal(QCreport$plots$ticplot_2$data[5,1], 536643304)
expect_equal(QCreport$plots$ticplot_3$data[6,3], 325)
expect_equal(QCreport$plots$ticplot_4$data$nPeak[7], 507)
expect_equal(QCreport$plots$ticplot_5$data$file.size[7], 3.56)
expect_equal(QCreport$plots$PCAallSamples$data$pc1[4], 6.47846949411406)
expect_equal(QCreport$plots$PCAQCsamples$data$pc2[5], 0.335577926713068)
expect_equal(QCreport$plots$PCAQCleading$data$pc1[4], 7.56288127255809)
expect_equal(QCreport$plots$PCAallQCleading$data$pc2[7], -7.24165986257958)
expect_equal(QCreport$plots$MAD_rt$data$list_object[34], 4.15956171093739)
expect_equal(QCreport$plots$peak_width$data$list_object[34],
46.808349609375)
expect_equal(QCreport$plots$mz_median$data$list_object[523],
-69.3985738677017)
expect_equal(QCreport$plots$EICs[[1]]$data$rt[34], 3554.39404296875)
expect_equal(QCreport$plots$EICs[[1]]$data$mz[45], 508.200012207031)
expect_equal(QCreport$plots$EICs[[1]]$data$i[45], 78184)
expect_equal(QCreport$plots$EICs[[1]]$data$Class[45],
structure(1L, .Label=c("QC", "Removed", "WT"), class = c("ordered",
"factor")))
expect_equal(QCreport$plots$EICs[[1]]$data$sample[45], 2L)
expect_equal(QCreport$plots$MVplot1$data$x[7], 17.910447761194)
expect_equal(QCreport$plots$MVplot2$data$x[10], 50)
expect_equal(QCreport$plots$MVplot3$data$class[6], 20.1492537313433)
expect_equal(QCreport$plots$MVplot4$data$class[531], 20)
expect_equal(QCreport$plots$RSDplot1$data$list_object[153],
42.1033162472477)
expect_equal(QCreport$plots$RSDplot2$data$RSD[97], 11.901710037869)
expect_equal(QCreport$plots$QCplot1$data$values[3], 0.126531150918856)
expect_equal(QCreport$plots$QCplot1$data$values[1123],
-0.00868209214666562)
expect_equal(QCreport$plots$QCplot2$data$value[3], 0.64753837592395)
expect_equal(QCreport$plots$QCplot2$data$value[1123], -0.380990238832714)
expect_equal(QCreport$plots$SBPCAbefore$data$pc1[4], 3.55062795302708)
expect_equal(QCreport$plots$SBPCAbeforeQC$data$pc1[3], 5.44564141304822)
expect_equal(QCreport$plots$SBRSDbefore$data$list_object[43],
26.0975634461339)
expect_equal(QCreport$plots$SBPCAfter$data$pc1[6], -0.370741378151436)
expect_equal(QCreport$plots$SBPCAfterQC$data$pc1[4], 5.89277901023488)
expect_equal(QCreport$plots$SBRSDafter$data$list_object[78],
2.30445829090211)
# Tables
expect_equal(QCreport$tables$corrMatrix[2, 1], -0.57)
expect_equal(QCreport$tables$corrMatrix[2, 2], 0.0650941627344147)
expect_equal(QCreport$tables$RT_rsd,
structure(list(
Min.=c(0.00318857359890208, 0.00511148124967863),
`1st Qu.`=c(0.0840254897400688, 0.115441585461868),
Median=c(0.136879091709147, 0.238908162172896),
Mean=c(0.285418323971856, 0.34243500053187),
`3rd Qu.`=c(0.367293950976682, 0.511650919161229),
Max.=c(2.29359102554849, 2.08891122720008),
`NA's`=c(8, 10)),
row.names=c("QC", "WT"),
class = "data.frame")
)
expect_equal(QCreport$tables$RT_mad,
structure(list(
Min.=c(0, 0),
`1st Qu.`=c(1.7177122716795, 2.31271664428711),
Median=c(3.7412484375, 5.00069831542969),
Mean=c(8.60809614984987, 9.08930910256126),
`3rd Qu.`=c(10.419011315918, 11.7209465881348),
Max.=c(112.605569384766, 55.1881199707031),
`NA's`=c(0, 4)),
row.names = c("QC", "WT"),
class = "data.frame")
)
expect_equal(QCreport$tables$peak_width,
structure(list(
Min.=c(12.33056640625, 7.738037109375),
`1st Qu.`=c(38.6731630859375, 39.0038757324219),
Median=c(47.4981689453125, 48.1656494140625),
Mean=c(48.9647423296117, 49.7862030954072),
`3rd Qu.`=c(56.3682250976562, 56.9166870117188),
Max.=c(146.4296875, 108.039428710938),
`NA's`=c(0, 4)),
row.names=c("QC", "WT"),
class="data.frame")
)
expect_equal(QCreport$tables$mz_median,
structure(list(
Min.=c(-272.227294755146, -284.60683892769),
`1st Qu.`=c(-21.3940776658473, 0),
Median=c(0, 0),
Mean=c(-12.9934795359947, 14.5174218106226),
`3rd Qu.`=c(0, 29.6237475668885),
Max.=c(120.794903450402, 223.103402367672),
`NA's`=c(0, 4)),
row.names=c("QC", "WT"),
class="data.frame")
)
expect_equal(QCreport$tables$RSDtable1[2, 4], 45.8166907329745)
expect_equal(QCreport$tables$SBtableBefore[1, 3], 32.9090168180649)
expect_equal(QCreport$tables$SBtableAfter[1, 3], 11.2174961555864)
# data
expect_equal(QCreport$data$PCAinF$Data[4, 5], 149097.550000002)
expect_equal(QCreport$data$PCAinF$classes[6], "WT")
expect_equal(QCreport$data$PCAinF$RSD$variability_method, "RSD")
expect_equal(names(QCreport$data$PCAinF$RSD$WT[34]), "305.1/2930")
expect_equal(QCreport$data$PCAinF$RSD$WT[45],
c(`315/2513`=61.1306994096235))
expect_equal(QCreport$data$PCAinF$RSD$WT[45],
c(`315/2513`=61.1306994096235))
expect_equal(QCreport$data$PCAinF$RSD$QC[45],
c(`315/2513` = 54.3657276849361))
expect_equal(QCreport$excludeQC, "remove")
expect_equivalent(QCreport$projectHeader[3, 2], "LCMS_xdata")
expect_equivalent(QCreport$projectHeader[6, 2], "11")
expect_equivalent(QCreport$projectHeader[7, 2], "QC, WT")
expect_equivalent(QCreport$peakPickingParams[1,2], "268")
expect_equivalent(QCreport$TICs[10], c(`11` = 575133855.059309))
expect_equivalent(QCreport$TICraw[1], 0)
expect_null(QCreport$TICdata[[3]])
expect_equivalent(QCreport$samp.sum[c(1, 5, 7), ],
data.frame(
Sample=c("ko15", "ko21", "wt16"),
`Measurement time`=as.character(c(NA, NA, NA)),
Class=c("QC", "QC", "WT"),
`Number of peaks`=c(561, 276, 507),
`mzML file size (MB)`=c(3.52, 3.58, 3.56),
check.names=FALSE)
)
expect_equal(QCreport$QC_hits, 1L:6L)
context("Test that QC report pdf file is created")
expect_warning(qcrms::createQCreport(QCreport))
expect_true(file.exists(file.path(temp_dir, "LCMS_xdata.pdf")))
expect_true(file.exists(file.path(temp_dir, "LCMS_xdata_EICs.pdf")))
expect_equal(QCreport$peakPickingParams,
structure(
c("Number of peak groups:", "method", "ppm", "peakwidth", "mzdif",
"snthresh", "integrate", "noise", "prefilter", "268",
"CentWave", "25", "20-80", "-0.001", "10", "1", "5000",
"3, 100"),
.Dim=c(9L, 2L), .Dimnames=list(NULL, c("", ""))
)
)
context("Using xlsx input for meta data returns the same output.")
expect_warning(QCreport <- createQCreportObject(
data_file="LCMS_xdata.Rdata", projectdir=temp_dir,
metaData_file="qcrms_meta_data.xlsx", xcms_output="xdata",
classLabel="sample_group", excludeQC="remove", msms_label="MSMS",
plot_eic=FALSE)
)
expect_equal(QCreport$metaData$file, "qcrms_meta_data.xlsx")
expect_equal(QCreport$metaData$table,
structure(list(
Sample=c("ko15", "ko16", "ko18", "ko19", "ko21", "ko22",
"wt16", "wt18", "wt19", "wt21", "wt22"),
sample_group=c("Removed", "QC", "QC", "QC", "QC", "QC", "WT", "WT",
"WT", "WT", "WT"),
remove=c(TRUE, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA),
injection_order=1:11, batch=c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L)),
row.names=c(1L, 2L, 3L, 4L, 5L, 6L, 8L, 9L, 10L, 11L, 12L),
class="data.frame")
)
context("Use classQC column to fill in missing sample labels. And reading
from metaData sheet in xlsx file. Locating raw data files in
different folder than xcms object.")
raw_paths <- QCreport$raw_paths
# On M$ Windows xcms keeps "\\"
raw_paths <- gsub("\\\\", "/", QCreport$raw_paths)
meta_data$ClassQC <- meta_data$sample_group
meta_data$sample_group[1:6] <- NA
addWorksheet (wb,"metaData")
writeData (wb,"metaData", meta_data, rowNames = F)
saveWorkbook (wb, file.path(temp_dir, "qcrms_meta_data.xlsx"),
overwrite = T)
expect_warning(QCreport <- createQCreportObject(
data_file="LCMS_xdata.Rdata", projectdir=temp_dir,
metaData_file="qcrms_meta_data.xlsx", xcms_output="xdata",
classLabel="sample_group", excludeQC="remove", msms_label="MSMS",
plot_eic=FALSE,
raw_path=system.file("cdf", package="faahKO"))
)
# Fails on travis, as apperantly packages can be installed in two different
# locations.
#Last 13 lines of output:
# x[3]: "/tmp/RtmpY18EPf/RLIBS_3ab6462428bf/faahKO/cdf/KO/ko18.CDF"
# y[3]: "/home/travis/R/Library/faahKO/cdf/KO/ko18.CDF"
# expect_equivalent(QCreport$raw_paths, file.path(raw_paths))
expect_equal(QCreport$metaData$file, "qcrms_meta_data.xlsx")
expect_equal(QCreport$metaData$table[, -4],
structure(list(
Sample=c("ko15", "ko16", "ko18", "ko19", "ko21", "ko22",
"wt16", "wt18", "wt19", "wt21", "wt22"),
sample_group=c("Removed", "QC", "QC", "QC", "QC", "QC", "WT", "WT",
"WT", "WT", "WT"),
remove=c(TRUE, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA),
injection_order=1:11, batch=c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L)),
row.names=c(1L, 2L, 3L, 4L, 5L, 6L, 8L, 9L, 10L, 11L, 12L),
class="data.frame")
)
context ("locate-raw-files returns error if can't locate raw files")
QCreport$raw_path <- system.file("cdf", "WT",package="faahKO")
expect_error(qcrms:::locate_raw_files(QCreportObject=QCreport),
regexp="Some or all raw data files couldn't be located in folder")
context ("If different file types are located in the raw data folder
return error.")
dir.create(file.path(temp_dir, "raw_files"))
file.create(file.path(temp_dir, "raw_files", "file1.mzML"))
file.create(file.path(temp_dir, "raw_files", "file2.CDF"))
QCreport$raw_path <- file.path(temp_dir, "raw_files")
expect_error(qcrms:::locate_raw_files(QCreport),
regexp="Some or all raw data files couldn't be located in folder")
context ("LCMS: Create metadata file from sample filenames.")
expect_warning(QCreport <- createQCreportObject(
data_file="LCMS_xdata.Rdata", projectdir=temp_dir, xcms_output="xdata",
classLabel="sample_group", excludeQC="remove", msms_label="MSMS",
plot_eic=FALSE, group_names=c("ko", "wt"), Blank_label=NULL,
QC_label=NULL)
)
expect_equal(QCreport$metaData$table,
structure(list(
Sample = c("ko15", "ko16", "ko18", "ko19", "ko21", "ko22", "wt15",
"wt16", "wt18", "wt19", "wt21", "wt22"),
sample_group = c("ko", "ko", "ko", "ko", "ko", "ko", "wt", "wt",
"wt", "wt", "wt", "wt"),
injection_order = 1:12),
row.names = c(NA, 12L),
class = "data.frame")
)
context ("LCMS: outputs using older xcmsSet class.")
xset <- xcmsSet(cdfs, method='centWave', ppm=25, peakwidth=c(20, 80),
snthresh=10, prefilter=c(3,100), integrate=1, mzdiff=-0.001,
verbose.columns=FALSE, fitgauss=FALSE, noise=5000)
# New xcms methods updates RT in peaks slot as well, that's not compatible
# with older xcmsSet
# xset <- xcms::retcor(xset, method="obiwarp", profStep=0.6, gapInit=0.3,
# gapExtend=2.4, localAlignment=FALSE)
xset@phenoData$class <- rep("S", 12)
xset <- xcms::group(xset, method="density", bw=30, minfrac=0.5, minsamp=1)
xdata <- xcms::findChromPeaks(raw_data, param=cwp)
xdata <- xcms::groupChromPeaks(xdata,
xcms::PeakDensityParam(sampleGroups=rep("S", 12)))
context ("Compare xcmsSet and XCMSnExp outputs.")
expect_equivalent(xcms::peaks(xset), xcms::chromPeaks(xdata))
expect_equivalent(xcms::groups(xset),
as.matrix(xcms::featureDefinitions(xdata)[, 1:8]))
expect_error(QCreport <- createQCreportObject(
data_file="LCMS_xdata.Rdata", projectdir=temp_dir,
metaData_file="qcrms_meta_data.xlsx", xcms_output="xset_oeer",
classLabel="sample_group", excludeQC="remove", msms_label="MSMS",
plot_eic=FALSE, assay="xset"), regexp="Please check that XCMS object"
)
save(file=file.path(temp_dir, "LCMS_xdata.Rdata"), list="xset")
expect_warning(QCreport <- createQCreportObject(
data_file="LCMS_xdata.Rdata", projectdir=temp_dir,
metaData_file="qcrms_meta_data.xlsx", xcms_output="xset",
classLabel="sample_group", excludeQC="remove", msms_label="MSMS",
plot_eic=FALSE, assay="xset")
)
expect_equal(QCreport$xcms_output, "xset")
expect_equivalent(QCreport$projectHeader[3, ], c("Assay:", "xset"))
expect_equal(QCreport$filtering$table,
structure(
list(Filter = c("Before filtering",
"Blank, fold_change=20, fraction=0",
"MV Sample, max_perc_mv=0.5",
"Features, method=QC, fraction=0.9",
"Featrues, method=across, fraction=0.5"),
`Number of features` = c(266L, 266L, 266L, 129L, 129L),
`Number of samples` = c(11L, 11L, 11L, 11L, 11L),
Applied = c(TRUE, FALSE, TRUE, TRUE, TRUE)),
row.names = c(NA, -5L), class = "data.frame")
)
unlink(file.path(temp_dir, "LCMS_xdata.Rdata"))
unlink(file.path(temp_dir, "qcrms_test_meta_data_file.csv"))
unlink(file.path(temp_dir, "LCMS_xdata.xlsx"))
unlink(file.path(temp_dir, "LCMS_xdata.pdf"))
unlink(file.path(temp_dir, "LCMS_xdata_EICs.pdf"))
unlink(file.path(temp_dir, "qcrms_meta_data.xlsx"))
unlink(file.path(temp_dir, "raw_files"), recursive=TRUE)
})
computational-metabolomics/qcrms documentation built on Jan. 18, 2021, 1:46 a.m.
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context("LCMS data")
library(xcms)
library(BiocManager)
if(!requireNamespace("msPurityData", quietly=TRUE)){
BiocManager::install("msPurityData")
}
if(!requireNamespace("faahKO", quietly=TRUE)){
BiocManager::install("faahKO")
}
test_that("createQCreportObject works with XCMS LCMS data outputs", {
require(xcms)
## Get the full path to the CDF files
cdfs <- dir(system.file("cdf", package="faahKO"), full.names=TRUE,
recursive=TRUE)
## Create a phenodata data.frame
meta_data <- data.frame(Sample=sub(basename(cdfs), pattern=".CDF",
replacement="", fixed=TRUE),
sample_group=c(rep("QC", 6), "MSMS",rep("WT", 5)),
remove=c(TRUE, rep(NA, 11)),
stringsAsFactors=FALSE)
rownames(meta_data) <- meta_data$Sample
expect_message(raw_data <- readMSData(files=cdfs,
pdata=new("NAnnotatedDataFrame", meta_data), mode="onDisk"))
cwp <- xcms::CentWaveParam(peakwidth = c(20, 80), noise=5000)
xdata <- xcms::findChromPeaks(raw_data, param=cwp)
xdata <- adjustRtime(xdata, param=ObiwarpParam(binSize=0.6))
xdata <- xcms::groupChromPeaks(xdata,
xcms::PeakDensityParam(sampleGroups=rep("S", 12)))
temp_dir <- tempdir()
write.csv(file=file.path(temp_dir, "qcrms_test_meta_data_file.csv"),
meta_data, row.names=F)
save(file=file.path(temp_dir, "LCMS_xdata.Rdata"), list="xdata")
# Create meta data xlsx file format
require (openxlsx)
wb <- createWorkbook()
addWorksheet (wb,"meta")
writeData (wb,"meta", meta_data, rowNames = F)
saveWorkbook (wb, file.path(temp_dir, "qcrms_meta_data.xlsx"),
overwrite = T)
expect_warning(QCreport <- createQCreportObject(
data_file="LCMS_xdata.Rdata", projectdir=temp_dir,
metaData_file="qcrms_test_meta_data_file.csv", xcms_output="xdata",
classLabel="sample_group", excludeQC="remove", msms_label="MSMS"))
expect_true(file.exists(file.path(temp_dir, "LCMS_xdata.xlsx")))
# Check content of output xlsx file
wb_temp <- openxlsx::loadWorkbook(file.path(temp_dir, "LCMS_xdata.xlsx"))
variableMetaData <- readWorkbook(wb_temp, "variableMetaData")
expect_equal(head (variableMetaData),
structure(list(name = c("M205T2791", "M206T2790", "M207T2719",
"M233T3029", "M241T3686", "M244T2835"),
mz=c(205, 206, 207.100006103516, 233, 241.100006103516,
244.100006103516),
mzmin=c(205, 206, 207.100006103516, 233, 241.100006103516,
244.100006103516),
mzmax=c(205, 206, 207.100006103516, 233, 241.199996948242,
244.100006103516),
rt=c(2791.04516601562, 2790.11202148437, 2718.83251953125,
3029.41455078125, 3686.39326269531, 2834.84826660156),
rtmin=c(2787.63159179688, 2786.41528320312, 2712.60815429688,
3014.683, 3671.52124023438, 2830.10083007812),
rtmax=c(2795.03662109375, 2795.61206054688, 2723.601,
3063.19799804688, 3740.9423828125, 2836.123046875),
npeaks=c(12, 12, 13, 11, 20, 6),
S=c(12, 11, 9, 9, 11, 6)),
row.names=c(NA, 6L), class="data.frame")
)
rm (wb_temp)
expect_equal(QCreport$xcms_output, "xdata")
expect_equal(QCreport$pca_scores_labels, "all")
expect_equal(QCreport$data_file, "LCMS_xdata.Rdata")
expect_equal(QCreport$projectdir, temp_dir)
expect_equal(QCreport$filtering$glog_lambda_filtered, 61043890464.6641)
expect_equal(QCreport$filtering$glog_lambda_filtered_SB, 1338305112712.85)
expect_equivalent(QCreport$filtering$table[c(1, 4), ],
data.frame(
Filter=c("Before filtering", "Features, method=QC, fraction=0.9"),
`Number of features`=c(268, 128),
`Number of samples`=c(11, 11),
Applied=c(TRUE, TRUE),
check.names=FALSE, stringsAsFactors=FALSE)
)
expect_equivalent(QCreport$xset@phenoData[c(1, 4, 9), ],
data.frame(
Sample=c("ko15", "ko19", "wt19"),
sample_group=c("QC", "QC", "WT"),
remove=c(TRUE, NA, NA),
class=c(1, 1, 1),
check.names=FALSE,
stringsAsFactors=FALSE)
)
expect_equivalent(QCreport$xset@peaks[1, ],
c(453.2000122, 453.2000122, 453.2000122, 2509.2795410, 2501.3779297,
2528.2773438, 1007408.9731765, 1007380.8042353, 38152.0000000,
38151.0000000, 1)
)
expect_equivalent(QCreport$xset@groups[13:14, ],
matrix(nrow=2, ncol=8, byrow=TRUE,
c(269.2000122, 269.100006, 269.2000122, 3889.45959, 3859.553467,
3900.083740, 16, 11, 279.0000000, 279.0000000, 279.0000000,
2790.799072, 2751.645508, 2801.754883, 19, 12
)
)
)
expect_equal(QCreport$xset@groupidx[[47]],
c(1405, 2436, 2854, 3896, 4299, 4982, 4990))
expect_equivalent(QCreport$xset@rt$raw[[5]][10:15],
c(2515.462, 2517.027, 2518.592, 2520.157, 2521.722, 2523.287))
expect_equivalent(QCreport$xset@rt$corrected[[5]][10:15],
c(2514.697510, 2516.180908, 2517.664795, 2519.149170, 2520.634277,
2522.120361))
expect_equal(QCreport$xset@.processHistory[[1]]@type, "Peak detection")
expect_equal(QCreport$xset@.processHistory[[1]]@param@ppm, 25)
expect_equal(QCreport$xset@.processHistory[[1]]@param@peakwidth, c(20, 80))
expect_equal(QCreport$xset@.processHistory[[1]]@param@snthresh, 10)
expect_equal(QCreport$xset@.processHistory[[1]]@param@mzdiff, -0.001)
expect_equal(QCreport$peakMatrix[1, 1:3],
c(ko15=1924712.01585714, ko16=1757150.9648, ko18=1714581.77647058))
expect_equal(QCreport$metaData$table,
structure(list(
Sample=c("ko15", "ko16", "ko18", "ko19", "ko21", "ko22",
"wt16", "wt18", "wt19", "wt21", "wt22"),
sample_group=c("Removed", "QC", "QC", "QC", "QC", "QC", "WT", "WT",
"WT", "WT", "WT"),
remove=c(TRUE, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA),
injection_order=1:11, batch=c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L)),
row.names=c(1L, 2L, 3L, 4L, 5L, 6L, 8L, 9L, 10L, 11L, 12L),
class="data.frame")
)
expect_equal(QCreport$pca_scores_labels, "all")
expect_equal(QCreport$metaData$classColumn, "sample_group")
# Plots
expect_equal(QCreport$plots$ticplot_1$data[3,1], 754424703.6)
expect_equal(QCreport$plots$ticplot_2$data[5,1], 536643304)
expect_equal(QCreport$plots$ticplot_3$data[6,3], 325)
expect_equal(QCreport$plots$ticplot_4$data$nPeak[7], 507)
expect_equal(QCreport$plots$ticplot_5$data$file.size[7], 3.56)
expect_equal(QCreport$plots$PCAallSamples$data$pc1[4], 6.47846949411406)
expect_equal(QCreport$plots$PCAQCsamples$data$pc2[5], 0.335577926713068)
expect_equal(QCreport$plots$PCAQCleading$data$pc1[4], 7.56288127255809)
expect_equal(QCreport$plots$PCAallQCleading$data$pc2[7], -7.24165986257958)
expect_equal(QCreport$plots$MAD_rt$data$list_object[34], 4.15956171093739)
expect_equal(QCreport$plots$peak_width$data$list_object[34],
46.808349609375)
expect_equal(QCreport$plots$mz_median$data$list_object[523],
-69.3985738677017)
expect_equal(QCreport$plots$EICs[[1]]$data$rt[34], 3554.39404296875)
expect_equal(QCreport$plots$EICs[[1]]$data$mz[45], 508.200012207031)
expect_equal(QCreport$plots$EICs[[1]]$data$i[45], 78184)
expect_equal(QCreport$plots$EICs[[1]]$data$Class[45],
structure(1L, .Label=c("QC", "Removed", "WT"), class = c("ordered",
"factor")))
expect_equal(QCreport$plots$EICs[[1]]$data$sample[45], 2L)
expect_equal(QCreport$plots$MVplot1$data$x[7], 17.910447761194)
expect_equal(QCreport$plots$MVplot2$data$x[10], 50)
expect_equal(QCreport$plots$MVplot3$data$class[6], 20.1492537313433)
expect_equal(QCreport$plots$MVplot4$data$class[531], 20)
expect_equal(QCreport$plots$RSDplot1$data$list_object[153],
42.1033162472477)
expect_equal(QCreport$plots$RSDplot2$data$RSD[97], 11.901710037869)
expect_equal(QCreport$plots$QCplot1$data$values[3], 0.126531150918856)
expect_equal(QCreport$plots$QCplot1$data$values[1123],
-0.00868209214666562)
expect_equal(QCreport$plots$QCplot2$data$value[3], 0.64753837592395)
expect_equal(QCreport$plots$QCplot2$data$value[1123], -0.380990238832714)
expect_equal(QCreport$plots$SBPCAbefore$data$pc1[4], 3.55062795302708)
expect_equal(QCreport$plots$SBPCAbeforeQC$data$pc1[3], 5.44564141304822)
expect_equal(QCreport$plots$SBRSDbefore$data$list_object[43],
26.0975634461339)
expect_equal(QCreport$plots$SBPCAfter$data$pc1[6], -0.370741378151436)
expect_equal(QCreport$plots$SBPCAfterQC$data$pc1[4], 5.89277901023488)
expect_equal(QCreport$plots$SBRSDafter$data$list_object[78],
2.30445829090211)
# Tables
expect_equal(QCreport$tables$corrMatrix[2, 1], -0.57)
expect_equal(QCreport$tables$corrMatrix[2, 2], 0.0650941627344147)
expect_equal(QCreport$tables$RT_rsd,
structure(list(
Min.=c(0.00318857359890208, 0.00511148124967863),
`1st Qu.`=c(0.0840254897400688, 0.115441585461868),
Median=c(0.136879091709147, 0.238908162172896),
Mean=c(0.285418323971856, 0.34243500053187),
`3rd Qu.`=c(0.367293950976682, 0.511650919161229),
Max.=c(2.29359102554849, 2.08891122720008),
`NA's`=c(8, 10)),
row.names=c("QC", "WT"),
class = "data.frame")
)
expect_equal(QCreport$tables$RT_mad,
structure(list(
Min.=c(0, 0),
`1st Qu.`=c(1.7177122716795, 2.31271664428711),
Median=c(3.7412484375, 5.00069831542969),
Mean=c(8.60809614984987, 9.08930910256126),
`3rd Qu.`=c(10.419011315918, 11.7209465881348),
Max.=c(112.605569384766, 55.1881199707031),
`NA's`=c(0, 4)),
row.names = c("QC", "WT"),
class = "data.frame")
)
expect_equal(QCreport$tables$peak_width,
structure(list(
Min.=c(12.33056640625, 7.738037109375),
`1st Qu.`=c(38.6731630859375, 39.0038757324219),
Median=c(47.4981689453125, 48.1656494140625),
Mean=c(48.9647423296117, 49.7862030954072),
`3rd Qu.`=c(56.3682250976562, 56.9166870117188),
Max.=c(146.4296875, 108.039428710938),
`NA's`=c(0, 4)),
row.names=c("QC", "WT"),
class="data.frame")
)
expect_equal(QCreport$tables$mz_median,
structure(list(
Min.=c(-272.227294755146, -284.60683892769),
`1st Qu.`=c(-21.3940776658473, 0),
Median=c(0, 0),
Mean=c(-12.9934795359947, 14.5174218106226),
`3rd Qu.`=c(0, 29.6237475668885),
Max.=c(120.794903450402, 223.103402367672),
`NA's`=c(0, 4)),
row.names=c("QC", "WT"),
class="data.frame")
)
expect_equal(QCreport$tables$RSDtable1[2, 4], 45.8166907329745)
expect_equal(QCreport$tables$SBtableBefore[1, 3], 32.9090168180649)
expect_equal(QCreport$tables$SBtableAfter[1, 3], 11.2174961555864)
# data
expect_equal(QCreport$data$PCAinF$Data[4, 5], 149097.550000002)
expect_equal(QCreport$data$PCAinF$classes[6], "WT")
expect_equal(QCreport$data$PCAinF$RSD$variability_method, "RSD")
expect_equal(names(QCreport$data$PCAinF$RSD$WT[34]), "305.1/2930")
expect_equal(QCreport$data$PCAinF$RSD$WT[45],
c(`315/2513`=61.1306994096235))
expect_equal(QCreport$data$PCAinF$RSD$WT[45],
c(`315/2513`=61.1306994096235))
expect_equal(QCreport$data$PCAinF$RSD$QC[45],
c(`315/2513` = 54.3657276849361))
expect_equal(QCreport$excludeQC, "remove")
expect_equivalent(QCreport$projectHeader[3, 2], "LCMS_xdata")
expect_equivalent(QCreport$projectHeader[6, 2], "11")
expect_equivalent(QCreport$projectHeader[7, 2], "QC, WT")
expect_equivalent(QCreport$peakPickingParams[1,2], "268")
expect_equivalent(QCreport$TICs[10], c(`11` = 575133855.059309))
expect_equivalent(QCreport$TICraw[1], 0)
expect_null(QCreport$TICdata[[3]])
expect_equivalent(QCreport$samp.sum[c(1, 5, 7), ],
data.frame(
Sample=c("ko15", "ko21", "wt16"),
`Measurement time`=as.character(c(NA, NA, NA)),
Class=c("QC", "QC", "WT"),
`Number of peaks`=c(561, 276, 507),
`mzML file size (MB)`=c(3.52, 3.58, 3.56),
check.names=FALSE)
)
expect_equal(QCreport$QC_hits, 1L:6L)
context("Test that QC report pdf file is created")
expect_warning(qcrms::createQCreport(QCreport))
expect_true(file.exists(file.path(temp_dir, "LCMS_xdata.pdf")))
expect_true(file.exists(file.path(temp_dir, "LCMS_xdata_EICs.pdf")))
expect_equal(QCreport$peakPickingParams,
structure(
c("Number of peak groups:", "method", "ppm", "peakwidth", "mzdif",
"snthresh", "integrate", "noise", "prefilter", "268",
"CentWave", "25", "20-80", "-0.001", "10", "1", "5000",
"3, 100"),
.Dim=c(9L, 2L), .Dimnames=list(NULL, c("", ""))
)
)
context("Using xlsx input for meta data returns the same output.")
expect_warning(QCreport <- createQCreportObject(
data_file="LCMS_xdata.Rdata", projectdir=temp_dir,
metaData_file="qcrms_meta_data.xlsx", xcms_output="xdata",
classLabel="sample_group", excludeQC="remove", msms_label="MSMS",
plot_eic=FALSE)
)
expect_equal(QCreport$metaData$file, "qcrms_meta_data.xlsx")
expect_equal(QCreport$metaData$table,
structure(list(
Sample=c("ko15", "ko16", "ko18", "ko19", "ko21", "ko22",
"wt16", "wt18", "wt19", "wt21", "wt22"),
sample_group=c("Removed", "QC", "QC", "QC", "QC", "QC", "WT", "WT",
"WT", "WT", "WT"),
remove=c(TRUE, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA),
injection_order=1:11, batch=c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L)),
row.names=c(1L, 2L, 3L, 4L, 5L, 6L, 8L, 9L, 10L, 11L, 12L),
class="data.frame")
)
context("Use classQC column to fill in missing sample labels. And reading
from metaData sheet in xlsx file. Locating raw data files in
different folder than xcms object.")
raw_paths <- QCreport$raw_paths
# On M$ Windows xcms keeps "\\"
raw_paths <- gsub("\\\\", "/", QCreport$raw_paths)
meta_data$ClassQC <- meta_data$sample_group
meta_data$sample_group[1:6] <- NA
addWorksheet (wb,"metaData")
writeData (wb,"metaData", meta_data, rowNames = F)
saveWorkbook (wb, file.path(temp_dir, "qcrms_meta_data.xlsx"),
overwrite = T)
expect_warning(QCreport <- createQCreportObject(
data_file="LCMS_xdata.Rdata", projectdir=temp_dir,
metaData_file="qcrms_meta_data.xlsx", xcms_output="xdata",
classLabel="sample_group", excludeQC="remove", msms_label="MSMS",
plot_eic=FALSE,
raw_path=system.file("cdf", package="faahKO"))
)
# Fails on travis, as apperantly packages can be installed in two different
# locations.
#Last 13 lines of output:
# x[3]: "/tmp/RtmpY18EPf/RLIBS_3ab6462428bf/faahKO/cdf/KO/ko18.CDF"
# y[3]: "/home/travis/R/Library/faahKO/cdf/KO/ko18.CDF"
# expect_equivalent(QCreport$raw_paths, file.path(raw_paths))
expect_equal(QCreport$metaData$file, "qcrms_meta_data.xlsx")
expect_equal(QCreport$metaData$table[, -4],
structure(list(
Sample=c("ko15", "ko16", "ko18", "ko19", "ko21", "ko22",
"wt16", "wt18", "wt19", "wt21", "wt22"),
sample_group=c("Removed", "QC", "QC", "QC", "QC", "QC", "WT", "WT",
"WT", "WT", "WT"),
remove=c(TRUE, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA),
injection_order=1:11, batch=c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L)),
row.names=c(1L, 2L, 3L, 4L, 5L, 6L, 8L, 9L, 10L, 11L, 12L),
class="data.frame")
)
context ("locate-raw-files returns error if can't locate raw files")
QCreport$raw_path <- system.file("cdf", "WT",package="faahKO")
expect_error(qcrms:::locate_raw_files(QCreportObject=QCreport),
regexp="Some or all raw data files couldn't be located in folder")
context ("If different file types are located in the raw data folder
return error.")
dir.create(file.path(temp_dir, "raw_files"))
file.create(file.path(temp_dir, "raw_files", "file1.mzML"))
file.create(file.path(temp_dir, "raw_files", "file2.CDF"))
QCreport$raw_path <- file.path(temp_dir, "raw_files")
expect_error(qcrms:::locate_raw_files(QCreport),
regexp="Some or all raw data files couldn't be located in folder")
context ("LCMS: Create metadata file from sample filenames.")
expect_warning(QCreport <- createQCreportObject(
data_file="LCMS_xdata.Rdata", projectdir=temp_dir, xcms_output="xdata",
classLabel="sample_group", excludeQC="remove", msms_label="MSMS",
plot_eic=FALSE, group_names=c("ko", "wt"), Blank_label=NULL,
QC_label=NULL)
)
expect_equal(QCreport$metaData$table,
structure(list(
Sample = c("ko15", "ko16", "ko18", "ko19", "ko21", "ko22", "wt15",
"wt16", "wt18", "wt19", "wt21", "wt22"),
sample_group = c("ko", "ko", "ko", "ko", "ko", "ko", "wt", "wt",
"wt", "wt", "wt", "wt"),
injection_order = 1:12),
row.names = c(NA, 12L),
class = "data.frame")
)
context ("LCMS: outputs using older xcmsSet class.")
xset <- xcmsSet(cdfs, method='centWave', ppm=25, peakwidth=c(20, 80),
snthresh=10, prefilter=c(3,100), integrate=1, mzdiff=-0.001,
verbose.columns=FALSE, fitgauss=FALSE, noise=5000)
# New xcms methods updates RT in peaks slot as well, that's not compatible
# with older xcmsSet
# xset <- xcms::retcor(xset, method="obiwarp", profStep=0.6, gapInit=0.3,
# gapExtend=2.4, localAlignment=FALSE)
xset@phenoData$class <- rep("S", 12)
xset <- xcms::group(xset, method="density", bw=30, minfrac=0.5, minsamp=1)
xdata <- xcms::findChromPeaks(raw_data, param=cwp)
xdata <- xcms::groupChromPeaks(xdata,
xcms::PeakDensityParam(sampleGroups=rep("S", 12)))
context ("Compare xcmsSet and XCMSnExp outputs.")
expect_equivalent(xcms::peaks(xset), xcms::chromPeaks(xdata))
expect_equivalent(xcms::groups(xset),
as.matrix(xcms::featureDefinitions(xdata)[, 1:8]))
expect_error(QCreport <- createQCreportObject(
data_file="LCMS_xdata.Rdata", projectdir=temp_dir,
metaData_file="qcrms_meta_data.xlsx", xcms_output="xset_oeer",
classLabel="sample_group", excludeQC="remove", msms_label="MSMS",
plot_eic=FALSE, assay="xset"), regexp="Please check that XCMS object"
)
save(file=file.path(temp_dir, "LCMS_xdata.Rdata"), list="xset")
expect_warning(QCreport <- createQCreportObject(
data_file="LCMS_xdata.Rdata", projectdir=temp_dir,
metaData_file="qcrms_meta_data.xlsx", xcms_output="xset",
classLabel="sample_group", excludeQC="remove", msms_label="MSMS",
plot_eic=FALSE, assay="xset")
)
expect_equal(QCreport$xcms_output, "xset")
expect_equivalent(QCreport$projectHeader[3, ], c("Assay:", "xset"))
expect_equal(QCreport$filtering$table,
structure(
list(Filter = c("Before filtering",
"Blank, fold_change=20, fraction=0",
"MV Sample, max_perc_mv=0.5",
"Features, method=QC, fraction=0.9",
"Featrues, method=across, fraction=0.5"),
`Number of features` = c(266L, 266L, 266L, 129L, 129L),
`Number of samples` = c(11L, 11L, 11L, 11L, 11L),
Applied = c(TRUE, FALSE, TRUE, TRUE, TRUE)),
row.names = c(NA, -5L), class = "data.frame")
)
unlink(file.path(temp_dir, "LCMS_xdata.Rdata"))
unlink(file.path(temp_dir, "qcrms_test_meta_data_file.csv"))
unlink(file.path(temp_dir, "LCMS_xdata.xlsx"))
unlink(file.path(temp_dir, "LCMS_xdata.pdf"))
unlink(file.path(temp_dir, "LCMS_xdata_EICs.pdf"))
unlink(file.path(temp_dir, "qcrms_meta_data.xlsx"))
unlink(file.path(temp_dir, "raw_files"), recursive=TRUE)
})
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