| e501fc3e |
## Testing to write stuff.
|
| 028e1f19 |
test_copyWriteMSData <- function() {
test_folder = tempdir()
|
| d4bcbe13 |
## INPUT: mzXML
|
| 19dc1af2 |
orig_file <- system.file("threonine", "threonine_i2_e35_pH_tree.mzXML",
|
| 7da97ca9 |
package = "msdata")
|
| 9a1512c8 |
mzML_xsd <- XML::xmlTreeParse(system.file("extdata", "mzML1.1.0.xsd",
package = "mzR"),
isSchema = TRUE, useInternal = TRUE)
mzML_xsd_idx <- XML::xmlTreeParse(system.file("extdata", "mzML1.1.2_idx.xsd",
package = "mzR"),
isSchema = TRUE, useInternal = TRUE)
|
| 19dc1af2 |
mzxml <- openMSfile(orig_file, backend = "pwiz")
|
| e501fc3e |
pks <- peaks(mzxml)
hdr <- header(mzxml)
|
| d4bcbe13 |
ii <- mzR::instrumentInfo(mzxml)
|
| e501fc3e |
mzR::close(mzxml)
|
| d4bcbe13 |
## OUTPUT: mzML
|
| e501fc3e |
fnew <- paste0(test_folder, "test_copyWrite.mzML")
|
| 7da97ca9 |
mzR::copyWriteMSData(file = fnew, original_file = orig_file,
header = hdr, object = pks, backend = "pwiz")
|
| 5afbbd4f |
## Check content is same
|
| e501fc3e |
mzml_new <- openMSfile(fnew, backend = "pwiz")
pks_new <- peaks(mzml_new)
hdr_new <- header(mzml_new)
|
| d4bcbe13 |
ii_new <- mzR::instrumentInfo(mzml_new)
|
| e501fc3e |
mzR::close(mzml_new)
|
| 5afbbd4f |
checkEquals(pks_new, pks)
|
| d4bcbe13 |
checkEquals(hdr_new, hdr)
checkEquals(ii, ii_new)
## OUTPUT: mzXML
fnew <- paste0(test_folder, "test_copyWrite.mzXML")
|
| 7da97ca9 |
mzR::copyWriteMSData(file = fnew, original_file = orig_file,
header = hdr, object = pks, backend = "pwiz",
outformat = "mzxml")
|
| d4bcbe13 |
## Check content is same
mzml_new <- openMSfile(fnew, backend = "pwiz")
pks_new <- peaks(mzml_new)
hdr_new <- header(mzml_new)
ii_new <- mzR::instrumentInfo(mzml_new)
mzR::close(mzml_new)
checkEquals(pks_new, pks)
|
| 630000b7 |
## Don't compare IDs since they are different.
checkEquals(hdr_new[, colnames(hdr_new) != "spectrumId"],
hdr[, colnames(hdr) != "spectrumId"])
|
| d4bcbe13 |
checkEquals(ii, ii_new)
|
| 5afbbd4f |
## Save as mgf
## fnew <- paste0(test_folder, "test_copyWrite.mgf")
|
| d4bcbe13 |
## mzR:::copyWriteMSData(filename = fnew, original_file = orig_file,
|
| 5afbbd4f |
## header = hdr, data = pks, backend = "pwiz",
## outformat = "mgf")
## ## Check content is same
## mzml_new <- openMSfile(fnew, backend = "pwiz")
## pks_new <- peaks(mzml_new)
## hdr_new <- header(mzml_new)
## mzR::close(mzml_new)
## checkEquals(pks_new, pks)
## checkEquals(hdr_new, hdr)
|
| e501fc3e |
## Now, let's pick selected spectra instead.
hdr_sub <- hdr[c(1, 3, 5), ]
pks_sub <- pks[c(1, 3, 5)]
|
| 5afbbd4f |
fnew <- paste0(test_folder, "test_copyWrite.mzML")
## index is not OK after subsetting
|
| 7da97ca9 |
checkException(mzR:::copyWriteMSData(file = fnew,
|
| d4bcbe13 |
original_file = orig_file,
|
| 7da97ca9 |
header = hdr_sub, object = pks_sub,
|
| 5afbbd4f |
backend = "pwiz"))
hdr_sub$seqNum <- seq_len(nrow(hdr_sub))
|
| 630000b7 |
## mzML
|
| 7da97ca9 |
mzR::copyWriteMSData(file = fnew, original_file = orig_file,
header = hdr_sub, object = pks_sub, backend = "pwiz",
outformat = "mzml")
|
| 630000b7 |
## Check content is same
mzml_new <- openMSfile(fnew, backend = "pwiz")
pks_new <- peaks(mzml_new)
hdr_new <- header(mzml_new)
rownames(hdr_new) <- NULL
rownames(hdr_sub) <- NULL
checkEquals(pks_new, pks_sub)
checkEquals(hdr_new, hdr_sub)
|
| a4b3e08f |
checkEquals(peaks(mzml_new, 2), pks[[3]])
mzR::close(mzml_new)
|
| 630000b7 |
## mzXML
|
| 7da97ca9 |
mzR::copyWriteMSData(file = fnew, original_file = orig_file,
header = hdr_sub, object = pks_sub, backend = "pwiz",
outformat = "mzxml")
|
| 5afbbd4f |
## Check content is same
mzml_new <- openMSfile(fnew, backend = "pwiz")
pks_new <- peaks(mzml_new)
hdr_new <- header(mzml_new)
mzR::close(mzml_new)
rownames(hdr_new) <- NULL
rownames(hdr_sub) <- NULL
|
| 630000b7 |
## acquisitionNum and precursorScanNum are expected to be different, same
## as spectrumId
hdr_new$acquisitionNum <- as.integer(factor(hdr_new$acquisitionNum))
hdr_sub$acquisitionNum <- as.integer(factor(hdr_sub$acquisitionNum))
hdr_new$precursorScanNum <- as.integer(factor(hdr_new$precursorScanNum))
hdr_sub$precursorScanNum <- as.integer(factor(hdr_sub$precursorScanNum))
hdr_new$spectrumId <- as.integer(factor(hdr_new$spectrumId))
hdr_sub$spectrumId <- as.integer(factor(hdr_sub$spectrumId))
|
| 5afbbd4f |
checkEquals(pks_new, pks_sub)
|
| 630000b7 |
checkEquals(hdr_new, hdr_sub)
|
| 5afbbd4f |
## Check errors
## wrong header.
## wrong spectra.
## wrong data processing.
|
| 7da97ca9 |
checkException(mzR::copyWriteMSData(file = fnew,
original_file = orig_file,
header = pks, object = hdr,
backend = "pwiz"))
checkException(mzR::copyWriteMSData(file = fnew,
original_file = orig_file,
header = hdr, object = hdr,
backend = "pwiz"))
checkException(mzR::copyWriteMSData(file = fnew,
original_file = "somefile",
header = hdr, object = pks,
backend = "pwiz"))
checkException(mzR::copyWriteMSData(file = fnew,
original_file = orig_file,
header = hdr, object = pks,
backend = "pwiz",
software_processing = c("other")))
|
| 5afbbd4f |
|
| d4bcbe13 |
## INPUT: mzML
|
| 5afbbd4f |
orig_file <- system.file("proteomics",
"TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.mzML.gz",
package = "msdata")
|
| d4bcbe13 |
fl <- openMSfile(orig_file, backend = "pwiz")
pks <- peaks(fl)
hdr <- header(fl)
ii <- mzR::instrumentInfo(fl)
mzR::close(fl)
|
| 5afbbd4f |
|
| d4bcbe13 |
## OUTPUT: mzML
|
| 5afbbd4f |
fnew <- paste0(test_folder, "test_copyWrite.mzML")
|
| 7da97ca9 |
mzR::copyWriteMSData(file = fnew, original_file = orig_file,
header = hdr, object = pks, backend = "pwiz")
|
| 5afbbd4f |
## Check content is same
mzml_new <- openMSfile(fnew, backend = "pwiz")
pks_new <- peaks(mzml_new)
hdr_new <- header(mzml_new)
|
| d4bcbe13 |
ii_new <- mzR::instrumentInfo(mzml_new)
|
| 5afbbd4f |
checkEquals(pks_new, pks)
checkEquals(hdr_new, hdr) ## polarity is OK here
|
| d4bcbe13 |
checkEquals(ii, ii_new)
|
| a4b3e08f |
checkEquals(peaks(mzml_new, 12), pks[[12]])
mzR::close(mzml_new)
|
| d4bcbe13 |
## OUTPUT: mzXML
fnew <- paste0(test_folder, "test_copyWrite.mzXML")
|
| 1ab173f6 |
suppressWarnings(
mzR::copyWriteMSData(file = fnew, original_file = orig_file,
header = hdr, object = pks, backend = "pwiz",
outformat = "mzxml")
)
|
| d4bcbe13 |
## Check content is same
mzml_new <- openMSfile(fnew, backend = "pwiz")
pks_new <- peaks(mzml_new)
hdr_new <- header(mzml_new)
ii_new <- mzR::instrumentInfo(mzml_new)
mzR::close(mzml_new)
checkEquals(pks_new, pks)
## acquisitionNum and precursorScanNum will be different, replace with
## factors - order and all has to be the same though.
|
| 630000b7 |
hdr_mod <- hdr
hdr_mod$acquisitionNum <- as.integer(factor(hdr$acquisitionNum))
hdr_mod$precursorScanNum <- as.integer(factor(hdr$precursorScanNum))
|
| d4bcbe13 |
hdr_new$acquisitionNum <- as.integer(factor(hdr_new$acquisitionNum))
hdr_new$precursorScanNum <- as.integer(factor(hdr_new$precursorScanNum))
|
| 630000b7 |
rt_col <- colnames(hdr_mod) == "retentionTime"
checkEquals(hdr_mod[, rt_col], hdr_new[, rt_col], tolerance = 0.01)
cn <- colnames(hdr)[!(colnames(hdr) %in% c("injectionTime", "retentionTime",
|
| 2edb9032 |
"filterString", "spectrumId",
|
| 52172a4d |
"isolationWindowTargetMZ",
"scanWindowLowerLimit",
"scanWindowUpperLimit"))]
|
| 630000b7 |
checkEquals(hdr_mod[, cn], hdr_new[, cn])
|
| d4bcbe13 |
## checkEquals(ii, ii_new)
|
| 630000b7 |
## Subset. These checks ensure that the scan - precursor scan are mapped
## correctly!
idx <- c(`1003` = 1, `1006` = 4, `1019` = 17, `1021` = 19, `1024` = 22,
`1026` = 24)
## 1: no precursor
## 2: 1 as precursor, 1003
## 3: no precursor
## 4: no precursor
## 5: 4 as precursor, 1021
## 6: 4 as precursor, 1021
hdr_sub <- hdr[idx, ]
pks_sub <- pks[idx]
hdr_sub$seqNum <- 1:nrow(hdr_sub)
fnew <- paste0(test_folder, "test_copyWrite.mzML")
|
| 7da97ca9 |
mzR::copyWriteMSData(file = fnew, original_file = orig_file,
header = hdr_sub, object = pks_sub, backend = "pwiz",
outformat = "mzml")
|
| 630000b7 |
## Check content is same
mzml_new <- openMSfile(fnew, backend = "pwiz")
pks_new <- peaks(mzml_new)
hdr_new <- header(mzml_new)
ii_new <- mzR::instrumentInfo(mzml_new)
mzR::close(mzml_new)
checkEquals(pks_new, pks_sub)
rownames(hdr_sub) <- NULL
rownames(hdr_new) <- NULL
checkEquals(hdr_new, hdr_sub) ## polarity is OK here
checkEquals(ii, ii_new)
## Subset with mzXML
fnew <- paste0(test_folder, "test_copyWrite.mzXML")
|
| 1ab173f6 |
suppressWarnings(
mzR::copyWriteMSData(file = fnew, original_file = orig_file,
header = hdr_sub, object = pks_sub, backend = "pwiz",
outformat = "mzxml")
)
|
| 630000b7 |
## Check content is same
mzml_new <- openMSfile(fnew, backend = "pwiz")
pks_new <- peaks(mzml_new)
hdr_new <- header(mzml_new)
ii_new <- mzR::instrumentInfo(mzml_new)
mzR::close(mzml_new)
checkEquals(pks_new, pks_sub)
rownames(hdr_sub) <- NULL
rownames(hdr_new) <- NULL
hdr_sub$acquisitionNum <- as.integer(factor(hdr_sub$acquisitionNum))
hdr_sub$precursorScanNum <- as.integer(factor(hdr_sub$precursorScanNum))
hdr_new$acquisitionNum <- as.integer(factor(hdr_new$acquisitionNum))
hdr_new$precursorScanNum <- as.integer(factor(hdr_new$precursorScanNum))
rt_col <- colnames(hdr_sub) == "retentionTime"
checkEquals(hdr_sub[, rt_col], hdr_new[, rt_col], tolerance = 0.01)
cn <- colnames(hdr_sub)[!(colnames(hdr_sub) %in% c("injectionTime",
"retentionTime",
|
| 9fd7959c |
"filterString",
|
| 2edb9032 |
"spectrumId",
|
| 52172a4d |
"isolationWindowTargetMZ",
"scanWindowLowerLimit",
"scanWindowUpperLimit"))]
|
| 630000b7 |
checkEquals(hdr_sub[, cn], hdr_new[, cn])
|
| d4bcbe13 |
## Other mzML:
test_file <- system.file("microtofq", "MM14.mzML", package = "msdata")
in_file <- openMSfile(test_file, backend = "pwiz")
hdr <- header(in_file)
pks <- peaks(in_file)
ii <- mzR::instrumentInfo(in_file)
mzR::close(in_file)
## mzML
out_file <- paste0(test_folder, "test_copyWrite.mzML")
|
| 7da97ca9 |
mzR::copyWriteMSData(file = out_file, original_file = test_file,
header = hdr, object = pks,
|
| 82debcef |
software_processing = c("MSnbase", "2.3.8", "MS:-1"))
|
| d4bcbe13 |
in_file <- openMSfile(out_file, backend = "pwiz")
hdr_2 <- header(in_file)
pks_2 <- peaks(in_file)
ii_2 <- mzR::instrumentInfo(in_file)
mzR::close(in_file)
checkEquals(hdr, hdr_2)
checkEquals(pks, pks_2)
checkEquals(ii, ii_2)
## mzXML output:
out_file <- paste0(test_folder, "test_copyWrite.mzXML")
|
| 7da97ca9 |
mzR::copyWriteMSData(file = out_file, original_file = test_file,
header = hdr, object = pks, outformat = "mzXML",
|
| 82debcef |
software_processing = c("MSnbase", "2.3.8", "MS:-1"))
|
| d4bcbe13 |
in_file <- openMSfile(out_file, backend = "pwiz")
hdr_2 <- header(in_file)
pks_2 <- peaks(in_file)
mzR::close(in_file)
|
| 52172a4d |
cn <- c("spectrumId", "scanWindowLowerLimit", "scanWindowUpperLimit")
checkEquals(hdr[, !(colnames(hdr) %in% cn)],
hdr_2[, !(colnames(hdr_2) %in% cn)])
|
| d4bcbe13 |
checkEquals(pks, pks_2)
checkEquals(ii, ii_2)
|
| e501fc3e |
}
|
| a4b3e08f |
test_writeMSData <- function() {
|
| 9a1512c8 |
mzML_xsd <- XML::xmlTreeParse(system.file("extdata", "mzML1.1.0.xsd",
package = "mzR"),
isSchema = TRUE, useInternal = TRUE)
mzML_xsd_idx <- XML::xmlTreeParse(system.file("extdata", "mzML1.1.2_idx.xsd",
package = "mzR"),
isSchema = TRUE, useInternal = TRUE)
mzXML_xsd_idx <- XML::xmlTreeParse(system.file("extdata",
"mzXML_idx_3.2.xsd.xml",
package = "mzR"),
isSchema = TRUE, useInternal = TRUE)
|
| 028e1f19 |
test_folder = tempdir()
|
| d4bcbe13 |
## Input: mzXML
|
| e501fc3e |
test_file <- system.file("threonine", "threonine_i2_e35_pH_tree.mzXML",
package = "msdata")
in_file <- openMSfile(test_file, backend = "pwiz")
hdr <- header(in_file)
pks <- peaks(in_file)
mzR::close(in_file)
|
| d4bcbe13 |
## mzML
|
| 9a1512c8 |
out_file <- paste0(test_folder, "/test_write.mzML")
|
| 7da97ca9 |
writeMSData(file = out_file, header = hdr, object = pks)
|
| e501fc3e |
in_file <- openMSfile(out_file, backend = "pwiz")
hdr_2 <- header(in_file)
pks_2 <- peaks(in_file)
|
| 5afbbd4f |
checkEquals(hdr, hdr_2)
|
| e501fc3e |
checkEquals(pks, pks_2)
|
| a4b3e08f |
checkEquals(peaks(in_file, 13), pks[[13]])
mzR::close(in_file)
|
| 9a1512c8 |
## validate mzML:
doc <- XML::xmlInternalTreeParse(out_file)
res <- XML::xmlSchemaValidate(mzML_xsd_idx, doc)
checkEquals(res$status, 0)
|
| e501fc3e |
## Test subsetting.
hdr_sub <- hdr[c(1, 3, 5), ]
hdr_sub$seqNum <- 1:nrow(hdr_sub)
pks_sub <- pks[c(1, 3, 5)]
|
| 7da97ca9 |
writeMSData(pks_sub, out_file, header = hdr_sub)
|
| e501fc3e |
in_file <- openMSfile(out_file)
hdr_sub_2 <- header(in_file)
pks_sub_2 <- peaks(in_file)
|
| 630000b7 |
checkEquals(pks_sub, pks_sub_2)
|
| a4b3e08f |
checkEquals(peaks(in_file, 3), pks[[5]])
mzR::close(in_file)
|
| 630000b7 |
## mzXML does not support spectrumId, thus acquisitionNum, precursorScanNum
## and spectrumId will be different, but their order and mapping has to be
## the same.
hdr_sub$acquisitionNum <- as.integer(factor(hdr_sub$acquisitionNum))
hdr_sub_2$acquisitionNum <- as.integer(factor(hdr_sub_2$acquisitionNum))
hdr_sub$precursorScanNum <- as.integer(factor(hdr_sub$precursorScanNum))
hdr_sub_2$precursorScanNum <- as.integer(factor(hdr_sub_2$precursorScanNum))
hdr_sub$spectrumId <- as.integer(factor(hdr_sub$spectrumId))
hdr_sub_2$spectrumId <- as.integer(factor(hdr_sub_2$spectrumId))
rownames(hdr_sub) <- NULL
checkEquals(hdr_sub, hdr_sub_2)
|
| 9a1512c8 |
## validate mzML:
doc <- XML::xmlInternalTreeParse(out_file)
res <- XML::xmlSchemaValidate(mzML_xsd_idx, doc)
checkEquals(res$status, 0)
|
| e501fc3e |
|
| 5afbbd4f |
## mzXML output:
|
| 9a1512c8 |
out_file <- paste0(test_folder, "/test_write.mzXML")
|
| 7da97ca9 |
writeMSData(file = out_file, header = hdr, object = pks,
outformat = "mzXML")
|
| d4bcbe13 |
in_file <- openMSfile(out_file, backend = "pwiz")
hdr_2 <- header(in_file)
pks_2 <- peaks(in_file)
mzR::close(in_file)
checkEquals(pks, pks_2)
|
| 630000b7 |
checkEquals(hdr[, colnames(hdr) != "spectrumId"],
hdr_2[, colnames(hdr_2) != "spectrumId"])
hdr_sub <- hdr[c(1, 3, 5), ]
hdr_sub$seqNum <- 1:nrow(hdr_sub)
pks_sub <- pks[c(1, 3, 5)]
|
| 7da97ca9 |
writeMSData(file = out_file, header = hdr_sub, object = pks_sub,
outformat = "mzXML")
|
| 630000b7 |
in_file <- openMSfile(out_file)
hdr_sub_2 <- header(in_file)
pks_sub_2 <- peaks(in_file)
mzR::close(in_file)
checkEquals(pks_sub, pks_sub_2)
## mzXML does not support spectrumId, thus acquisitionNum, precursorScanNum
## and spectrumId will be different, but their order and mapping has to be
## the same.
hdr_sub$acquisitionNum <- as.integer(factor(hdr_sub$acquisitionNum))
hdr_sub_2$acquisitionNum <- as.integer(factor(hdr_sub_2$acquisitionNum))
hdr_sub$precursorScanNum <- as.integer(factor(hdr_sub$precursorScanNum))
hdr_sub_2$precursorScanNum <- as.integer(factor(hdr_sub_2$precursorScanNum))
hdr_sub$spectrumId <- as.integer(factor(hdr_sub$spectrumId))
hdr_sub_2$spectrumId <- as.integer(factor(hdr_sub_2$spectrumId))
rownames(hdr_sub) <- NULL
checkEquals(hdr_sub, hdr_sub_2)
|
| d4bcbe13 |
## mgf output:
## out_file <- paste0(test_folder, "test_write.mgf")
|
| 5afbbd4f |
## mzR:::writeMSData(filename = out_file, header = hdr, data = pks,
|
| d4bcbe13 |
## outformat = "mgf")
|
| 5afbbd4f |
## in_file <- openMSfile(out_file, backend = "pwiz")
## hdr_2 <- header(in_file)
## pks_2 <- peaks(in_file)
## mzR::close(in_file)
## checkEquals(hdr, hdr_2)
## checkEquals(pks, pks_2)
|
| d4bcbe13 |
## Input: mzML
test_file <- system.file("proteomics",
"TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.mzML.gz",
package = "msdata")
in_file <- openMSfile(test_file, backend = "pwiz")
hdr <- header(in_file)
pks <- peaks(in_file)
mzR::close(in_file)
## mzML
|
| 9a1512c8 |
out_file <- paste0(test_folder, "/test_write.mzML")
|
| 7da97ca9 |
writeMSData(pks, file = out_file, header = hdr)
|
| d4bcbe13 |
in_file <- openMSfile(out_file, backend = "pwiz")
hdr_2 <- header(in_file)
pks_2 <- peaks(in_file)
mzR::close(in_file)
checkEquals(pks, pks_2)
|
| 630000b7 |
## Don't understand exactly why, but here we do have different
## acquisitionNum and precursorScanNum while having the same spectrumID.
hdr_mod <- hdr
hdr_mod$acquisitionNum <- as.integer(factor(hdr_mod$acquisitionNum))
hdr_mod$precursorScanNum <- as.integer(factor(hdr_mod$precursorScanNum))
hdr_2$acquisitionNum <- as.integer(factor(hdr_2$acquisitionNum))
hdr_2$precursorScanNum <- as.integer(factor(hdr_2$precursorScanNum))
checkEquals(hdr_mod, hdr_2)
|
| 9a1512c8 |
## validate mzML:
doc <- XML::xmlInternalTreeParse(out_file)
res <- XML::xmlSchemaValidate(mzML_xsd_idx, doc)
checkEquals(res$status, 0)
|
| d4bcbe13 |
## mzXML output:
|
| 9a1512c8 |
out_file <- paste0(test_folder, "/test_write.mzXML")
|
| a4b3e08f |
suppressWarnings(
writeMSData(file = out_file, header = hdr, object = pks,
outformat = "mzXML")
)
|
| d4bcbe13 |
in_file <- openMSfile(out_file, backend = "pwiz")
hdr_2 <- header(in_file)
pks_2 <- peaks(in_file)
mzR::close(in_file)
rt_col <- which(colnames(hdr) == "retentionTime")
checkEquals(hdr[, rt_col], hdr_2[, rt_col], tolerance = 0.01)
checkEquals(pks, pks_2)
|
| 630000b7 |
hdr_mod <- hdr
hdr_mod$acquisitionNum <- as.integer(factor(hdr_mod$acquisitionNum))
hdr_mod$precursorScanNum <- as.integer(factor(hdr_mod$precursorScanNum))
hdr_2$acquisitionNum <- as.integer(factor(hdr_2$acquisitionNum))
hdr_2$precursorScanNum <- as.integer(factor(hdr_2$precursorScanNum))
cn <- colnames(hdr_mod)[!(colnames(hdr_mod) %in% c("retentionTime",
"injectionTime",
|
| 9fd7959c |
"filterString",
|
| 2edb9032 |
"spectrumId",
|
| 52172a4d |
"isolationWindowTargetMZ",
"scanWindowLowerLimit",
"scanWindowUpperLimit"))]
|
| 630000b7 |
checkEquals(hdr_mod[, cn], hdr_2[, cn])
## Subset. These checks ensure that the scan - precursor scan are mapped
## correctly!
idx <- c(`1003` = 1, `1006` = 4, `1019` = 17, `1021` = 19, `1024` = 22,
`1026` = 24)
## 1: no precursor
## 2: 1 as precursor, 1003
## 3: no precursor
## 4: no precursor
## 5: 4 as precursor, 1021
## 6: 4 as precursor, 1021
hdr_sub <- hdr[idx, ]
rownames(hdr_sub) <- NULL
hdr_sub$seqNum <- 1:nrow(hdr_sub)
pks_sub <- pks[idx]
fnew <- paste0(test_folder, "test_copyWrite.mzML")
|
| 7da97ca9 |
writeMSData(file = fnew,
header = hdr_sub, object = pks_sub, backend = "pwiz",
outformat = "mzml")
|
| 630000b7 |
## Check content is same
mzml_new <- openMSfile(fnew, backend = "pwiz")
pks_new <- peaks(mzml_new)
hdr_new <- header(mzml_new)
ii_new <- mzR::instrumentInfo(mzml_new)
mzR::close(mzml_new)
checkEquals(pks_new, pks_sub)
## I don't quite understand that, but the acquisitionNum and the
## precursorScanNum are different while the spectrumId is the same.
## Still, check that the precursorScanNum is what we expect:
|
| 2c7479f5 |
checkEquals(hdr_new$precursorScanNum, c(NA, 1, NA, NA, 4, 4))
|
| 630000b7 |
hdr_new$acquisitionNum <- as.integer(factor(hdr_new$acquisitionNum))
hdr_new$precursorScanNum <- as.integer(factor(hdr_new$precursorScanNum))
hdr_sub$acquisitionNum <- as.integer(factor(hdr_sub$acquisitionNum))
hdr_sub$precursorScanNum <- as.integer(factor(hdr_sub$precursorScanNum))
checkEquals(hdr_new, hdr_sub) ## polarity is OK here
|
| d4bcbe13 |
|
| 630000b7 |
## Subset with mzXML
hdr_sub <- hdr[idx, ]
rownames(hdr_sub) <- NULL
hdr_sub$seqNum <- 1:nrow(hdr_sub)
pks_sub <- pks[idx]
fnew <- paste0(test_folder, "test_copyWrite.mzXML")
|
| a4b3e08f |
suppressWarnings(
writeMSData(file = fnew, header = hdr_sub, object = pks_sub,
backend = "pwiz", outformat = "mzxml")
)
|
| 630000b7 |
## Check content is same
mzml_new <- openMSfile(fnew, backend = "pwiz")
pks_new <- peaks(mzml_new)
hdr_new <- header(mzml_new)
ii_new <- mzR::instrumentInfo(mzml_new)
mzR::close(mzml_new)
checkEquals(pks_new, pks_sub)
|
| 2c7479f5 |
checkEquals(hdr_new$precursorScanNum, c(NA, 1, NA, NA, 4, 4))
|
| 630000b7 |
rownames(hdr_sub) <- NULL
rownames(hdr_new) <- NULL
hdr_sub$acquisitionNum <- as.integer(factor(hdr_sub$acquisitionNum))
hdr_sub$precursorScanNum <- as.integer(factor(hdr_sub$precursorScanNum))
hdr_new$acquisitionNum <- as.integer(factor(hdr_new$acquisitionNum))
hdr_new$precursorScanNum <- as.integer(factor(hdr_new$precursorScanNum))
rt_col <- colnames(hdr_sub) == "retentionTime"
checkEquals(hdr_sub[, rt_col], hdr_new[, rt_col], tolerance = 0.01)
cn <- colnames(hdr_sub)[!(colnames(hdr_sub) %in% c("injectionTime",
"retentionTime",
|
| 9fd7959c |
"filterString",
|
| 2edb9032 |
"spectrumId",
|
| 52172a4d |
"isolationWindowTargetMZ",
"scanWindowLowerLimit",
"scanWindowUpperLimit"))]
|
| 630000b7 |
checkEquals(hdr_sub[, cn], hdr_new[, cn])
|
| d4bcbe13 |
## Other mzML:
test_file <- system.file("microtofq", "MM14.mzML", package = "msdata")
in_file <- openMSfile(test_file, backend = "pwiz")
hdr <- header(in_file)
pks <- peaks(in_file)
mzR::close(in_file)
## mzML
|
| 9a1512c8 |
out_file <- paste0(test_folder, "/test_write.mzML")
|
| 7da97ca9 |
writeMSData(file = out_file, header = hdr, object = pks)
|
| d4bcbe13 |
in_file <- openMSfile(out_file, backend = "pwiz")
hdr_2 <- header(in_file)
pks_2 <- peaks(in_file)
mzR::close(in_file)
checkEquals(hdr, hdr_2)
checkEquals(pks, pks_2)
|
| 9a1512c8 |
## validate mzML:
doc <- XML::xmlInternalTreeParse(out_file)
res <- XML::xmlSchemaValidate(mzML_xsd_idx, doc)
checkEquals(res$status, 0)
|
| d4bcbe13 |
## mzXML output:
out_file <- paste0(test_folder, "test_write.mzXML")
|
| 7da97ca9 |
writeMSData(file = out_file, header = hdr, object = pks,
outformat = "mzXML")
|
| d4bcbe13 |
in_file <- openMSfile(out_file, backend = "pwiz")
hdr_2 <- header(in_file)
pks_2 <- peaks(in_file)
mzR::close(in_file)
checkEquals(pks, pks_2)
|
| 52172a4d |
cn <- c("spectrumId", "scanWindowLowerLimit", "scanWindowUpperLimit")
checkEquals(hdr[, !(colnames(hdr_2) %in% cn)],
|
| e3f79ff5 |
hdr_2[, !(colnames(hdr_2) %in% cn)])
|
| e501fc3e |
}
|
