jorainer authored on 20/09/2021 12:19:56
| ... | ... |
@@ -122,10 +122,6 @@ test_copyWriteMSData <- function() {
|
| 122 | 122 |
original_file = orig_file, |
| 123 | 123 |
header = hdr, object = hdr, |
| 124 | 124 |
backend = "pwiz")) |
| 125 |
- checkException(mzR::copyWriteMSData(file = fnew, |
|
| 126 |
- original_file = orig_file, |
|
| 127 |
- header = hdr, object = pks, |
|
| 128 |
- backend = "Ramp")) |
|
| 129 | 125 |
checkException(mzR::copyWriteMSData(file = fnew, |
| 130 | 126 |
original_file = "somefile", |
| 131 | 127 |
header = hdr, object = pks, |
| ... | ... |
@@ -556,51 +552,5 @@ test_writeMSData <- function() {
|
| 556 | 552 |
checkEquals(pks, pks_2) |
| 557 | 553 |
cn <- c("spectrumId", "scanWindowLowerLimit", "scanWindowUpperLimit")
|
| 558 | 554 |
checkEquals(hdr[, !(colnames(hdr_2) %in% cn)], |
| 559 |
- hdr_2[, !(colnames(hdr_2) %in% cn)]) |
|
| 560 |
- |
|
| 561 |
- ## mzData: |
|
| 562 |
- test_file <- system.file("iontrap", "extracted.mzData", package = "msdata")
|
|
| 563 |
- in_file <- openMSfile(test_file, backend = "Ramp") |
|
| 564 |
- hdr <- header(in_file) |
|
| 565 |
- hdr_orig <- hdr |
|
| 566 |
- pks <- peaks(in_file) |
|
| 567 |
- mzR::close(in_file) |
|
| 568 |
- |
|
| 569 |
- ## mzML |
|
| 570 |
- out_file <- paste0(test_folder, "/test_write.mzML") |
|
| 571 |
- writeMSData(file = out_file, header = hdr_orig, object = pks) |
|
| 572 |
- in_file <- openMSfile(out_file, backend = "pwiz") |
|
| 573 |
- hdr_2 <- header(in_file) |
|
| 574 |
- pks_2 <- peaks(in_file) |
|
| 575 |
- mzR::close(in_file) |
|
| 576 |
- hdr <- data.frame(lapply(hdr, function(z) {
|
|
| 577 |
- z[is.na(z)] <- 0 |
|
| 578 |
- z |
|
| 579 |
- })) |
|
| 580 |
- hdr_2 <- data.frame(lapply(hdr_2, function(z) {
|
|
| 581 |
- z[is.na(z)] <- 0 |
|
| 582 |
- z |
|
| 583 |
- })) |
|
| 584 |
- checkEquals(hdr, hdr_2) |
|
| 585 |
- checkEquals(pks, pks_2) |
|
| 586 |
- ## validate mzML: |
|
| 587 |
- doc <- XML::xmlInternalTreeParse(out_file) |
|
| 588 |
- res <- XML::xmlSchemaValidate(mzML_xsd_idx, doc) |
|
| 589 |
- checkEquals(res$status, 0) |
|
| 590 |
- |
|
| 591 |
- ## mzXML output: |
|
| 592 |
- out_file <- paste0(test_folder, "test_write.mzXML") |
|
| 593 |
- writeMSData(file = out_file, header = hdr_orig, object = pks, |
|
| 594 |
- outformat = "mzXML") |
|
| 595 |
- in_file <- openMSfile(out_file, backend = "pwiz") |
|
| 596 |
- hdr_2 <- header(in_file) |
|
| 597 |
- hdr_2 <- data.frame(lapply(hdr_2, function(z) {
|
|
| 598 |
- z[is.na(z)] <- 0 |
|
| 599 |
- z |
|
| 600 |
- })) |
|
| 601 |
- pks_2 <- peaks(in_file) |
|
| 602 |
- mzR::close(in_file) |
|
| 603 |
- checkEquals(pks, pks_2) |
|
| 604 |
- checkEquals(hdr[, colnames(hdr_2) != "centroided"], |
|
| 605 |
- hdr_2[, colnames(hdr_2) != "centroided"]) |
|
| 555 |
+ hdr_2[, !(colnames(hdr_2) %in% cn)]) |
|
| 606 | 556 |
} |
jorainer authored on 24/09/2019 20:03:58
| ... | ... |
@@ -601,6 +601,6 @@ test_writeMSData <- function() {
|
| 601 | 601 |
pks_2 <- peaks(in_file) |
| 602 | 602 |
mzR::close(in_file) |
| 603 | 603 |
checkEquals(pks, pks_2) |
| 604 |
- hdr$centroided <- FALSE |
|
| 605 |
- checkEquals(hdr, hdr_2) |
|
| 604 |
+ checkEquals(hdr[, colnames(hdr_2) != "centroided"], |
|
| 605 |
+ hdr_2[, colnames(hdr_2) != "centroided"]) |
|
| 606 | 606 |
} |
jorainer authored on 24/09/2019 16:50:18
| ... | ... |
@@ -482,7 +482,7 @@ test_writeMSData <- function() {
|
| 482 | 482 |
## I don't quite understand that, but the acquisitionNum and the |
| 483 | 483 |
## precursorScanNum are different while the spectrumId is the same. |
| 484 | 484 |
## Still, check that the precursorScanNum is what we expect: |
| 485 |
- checkEquals(hdr_new$precursorScanNum, c(0, 1, 0, 0, 4, 4)) |
|
| 485 |
+ checkEquals(hdr_new$precursorScanNum, c(NA, 1, NA, NA, 4, 4)) |
|
| 486 | 486 |
hdr_new$acquisitionNum <- as.integer(factor(hdr_new$acquisitionNum)) |
| 487 | 487 |
hdr_new$precursorScanNum <- as.integer(factor(hdr_new$precursorScanNum)) |
| 488 | 488 |
hdr_sub$acquisitionNum <- as.integer(factor(hdr_sub$acquisitionNum)) |
| ... | ... |
@@ -506,7 +506,7 @@ test_writeMSData <- function() {
|
| 506 | 506 |
ii_new <- mzR::instrumentInfo(mzml_new) |
| 507 | 507 |
mzR::close(mzml_new) |
| 508 | 508 |
checkEquals(pks_new, pks_sub) |
| 509 |
- checkEquals(hdr_new$precursorScanNum, c(0, 1, 0, 0, 4, 4)) |
|
| 509 |
+ checkEquals(hdr_new$precursorScanNum, c(NA, 1, NA, NA, 4, 4)) |
|
| 510 | 510 |
rownames(hdr_sub) <- NULL |
| 511 | 511 |
rownames(hdr_new) <- NULL |
| 512 | 512 |
hdr_sub$acquisitionNum <- as.integer(factor(hdr_sub$acquisitionNum)) |
| ... | ... |
@@ -562,16 +562,25 @@ test_writeMSData <- function() {
|
| 562 | 562 |
test_file <- system.file("iontrap", "extracted.mzData", package = "msdata")
|
| 563 | 563 |
in_file <- openMSfile(test_file, backend = "Ramp") |
| 564 | 564 |
hdr <- header(in_file) |
| 565 |
+ hdr_orig <- hdr |
|
| 565 | 566 |
pks <- peaks(in_file) |
| 566 | 567 |
mzR::close(in_file) |
| 567 | 568 |
|
| 568 | 569 |
## mzML |
| 569 | 570 |
out_file <- paste0(test_folder, "/test_write.mzML") |
| 570 |
- writeMSData(file = out_file, header = hdr, object = pks) |
|
| 571 |
+ writeMSData(file = out_file, header = hdr_orig, object = pks) |
|
| 571 | 572 |
in_file <- openMSfile(out_file, backend = "pwiz") |
| 572 | 573 |
hdr_2 <- header(in_file) |
| 573 | 574 |
pks_2 <- peaks(in_file) |
| 574 | 575 |
mzR::close(in_file) |
| 576 |
+ hdr <- data.frame(lapply(hdr, function(z) {
|
|
| 577 |
+ z[is.na(z)] <- 0 |
|
| 578 |
+ z |
|
| 579 |
+ })) |
|
| 580 |
+ hdr_2 <- data.frame(lapply(hdr_2, function(z) {
|
|
| 581 |
+ z[is.na(z)] <- 0 |
|
| 582 |
+ z |
|
| 583 |
+ })) |
|
| 575 | 584 |
checkEquals(hdr, hdr_2) |
| 576 | 585 |
checkEquals(pks, pks_2) |
| 577 | 586 |
## validate mzML: |
| ... | ... |
@@ -581,10 +590,14 @@ test_writeMSData <- function() {
|
| 581 | 590 |
|
| 582 | 591 |
## mzXML output: |
| 583 | 592 |
out_file <- paste0(test_folder, "test_write.mzXML") |
| 584 |
- writeMSData(file = out_file, header = hdr, object = pks, |
|
| 593 |
+ writeMSData(file = out_file, header = hdr_orig, object = pks, |
|
| 585 | 594 |
outformat = "mzXML") |
| 586 | 595 |
in_file <- openMSfile(out_file, backend = "pwiz") |
| 587 | 596 |
hdr_2 <- header(in_file) |
| 597 |
+ hdr_2 <- data.frame(lapply(hdr_2, function(z) {
|
|
| 598 |
+ z[is.na(z)] <- 0 |
|
| 599 |
+ z |
|
| 600 |
+ })) |
|
| 588 | 601 |
pks_2 <- peaks(in_file) |
| 589 | 602 |
mzR::close(in_file) |
| 590 | 603 |
checkEquals(pks, pks_2) |
- Add scanWindowLowerLimit and scanWindowUpperLimit variables.
- Export scanWindowLowerLimit and scanWindowUpperLimit to mzML (issue #202).
- Update and amend documentation and unit tests accordingly.
jorainer authored on 23/08/2019 14:02:46
| ... | ... |
@@ -186,7 +186,9 @@ test_copyWriteMSData <- function() {
|
| 186 | 186 |
checkEquals(hdr_mod[, rt_col], hdr_new[, rt_col], tolerance = 0.01) |
| 187 | 187 |
cn <- colnames(hdr)[!(colnames(hdr) %in% c("injectionTime", "retentionTime",
|
| 188 | 188 |
"filterString", "spectrumId", |
| 189 |
- "isolationWindowTargetMZ"))] |
|
| 189 |
+ "isolationWindowTargetMZ", |
|
| 190 |
+ "scanWindowLowerLimit", |
|
| 191 |
+ "scanWindowUpperLimit"))] |
|
| 190 | 192 |
checkEquals(hdr_mod[, cn], hdr_new[, cn]) |
| 191 | 193 |
## checkEquals(ii, ii_new) |
| 192 | 194 |
|
| ... | ... |
@@ -245,7 +247,9 @@ test_copyWriteMSData <- function() {
|
| 245 | 247 |
"retentionTime", |
| 246 | 248 |
"filterString", |
| 247 | 249 |
"spectrumId", |
| 248 |
- "isolationWindowTargetMZ"))] |
|
| 250 |
+ "isolationWindowTargetMZ", |
|
| 251 |
+ "scanWindowLowerLimit", |
|
| 252 |
+ "scanWindowUpperLimit"))] |
|
| 249 | 253 |
checkEquals(hdr_sub[, cn], hdr_new[, cn]) |
| 250 | 254 |
|
| 251 | 255 |
## Other mzML: |
| ... | ... |
@@ -279,8 +283,9 @@ test_copyWriteMSData <- function() {
|
| 279 | 283 |
hdr_2 <- header(in_file) |
| 280 | 284 |
pks_2 <- peaks(in_file) |
| 281 | 285 |
mzR::close(in_file) |
| 282 |
- checkEquals(hdr[, colnames(hdr) != "spectrumId"], |
|
| 283 |
- hdr_2[, colnames(hdr_2) != "spectrumId"]) |
|
| 286 |
+ cn <- c("spectrumId", "scanWindowLowerLimit", "scanWindowUpperLimit")
|
|
| 287 |
+ checkEquals(hdr[, !(colnames(hdr) %in% cn)], |
|
| 288 |
+ hdr_2[, !(colnames(hdr_2) %in% cn)]) |
|
| 284 | 289 |
checkEquals(pks, pks_2) |
| 285 | 290 |
checkEquals(ii, ii_2) |
| 286 | 291 |
} |
| ... | ... |
@@ -444,7 +449,9 @@ test_writeMSData <- function() {
|
| 444 | 449 |
"injectionTime", |
| 445 | 450 |
"filterString", |
| 446 | 451 |
"spectrumId", |
| 447 |
- "isolationWindowTargetMZ"))] |
|
| 452 |
+ "isolationWindowTargetMZ", |
|
| 453 |
+ "scanWindowLowerLimit", |
|
| 454 |
+ "scanWindowUpperLimit"))] |
|
| 448 | 455 |
checkEquals(hdr_mod[, cn], hdr_2[, cn]) |
| 449 | 456 |
|
| 450 | 457 |
## Subset. These checks ensure that the scan - precursor scan are mapped |
| ... | ... |
@@ -512,7 +519,9 @@ test_writeMSData <- function() {
|
| 512 | 519 |
"retentionTime", |
| 513 | 520 |
"filterString", |
| 514 | 521 |
"spectrumId", |
| 515 |
- "isolationWindowTargetMZ"))] |
|
| 522 |
+ "isolationWindowTargetMZ", |
|
| 523 |
+ "scanWindowLowerLimit", |
|
| 524 |
+ "scanWindowUpperLimit"))] |
|
| 516 | 525 |
checkEquals(hdr_sub[, cn], hdr_new[, cn]) |
| 517 | 526 |
|
| 518 | 527 |
## Other mzML: |
| ... | ... |
@@ -545,9 +554,10 @@ test_writeMSData <- function() {
|
| 545 | 554 |
pks_2 <- peaks(in_file) |
| 546 | 555 |
mzR::close(in_file) |
| 547 | 556 |
checkEquals(pks, pks_2) |
| 548 |
- checkEquals(hdr[, colnames(hdr_2) != "spectrumId"], |
|
| 549 |
- hdr_2[, colnames(hdr_2) != "spectrumId"]) |
|
| 550 |
- |
|
| 557 |
+ cn <- c("spectrumId", "scanWindowLowerLimit", "scanWindowUpperLimit")
|
|
| 558 |
+ checkEquals(hdr[, !(colnames(hdr_2) %in% cn)], |
|
| 559 |
+ hdr_2[, !(colnames(hdr_2) %in% cn)]) |
|
| 560 |
+ |
|
| 551 | 561 |
## mzData: |
| 552 | 562 |
test_file <- system.file("iontrap", "extracted.mzData", package = "msdata")
|
| 553 | 563 |
in_file <- openMSfile(test_file, backend = "Ramp") |
- Extract isolation window from mzML files (issue #193): data.frame returned by
jeader gains columns "isolationWindowTargetMZ", "isolationWindowLowerOffset"
and "isolationWindowUpperOffset" enabling SWATH data analysis.
- Adapt documentation and unit tests.
jotsetung authored on 03/04/2019 09:40:16
| ... | ... |
@@ -185,7 +185,8 @@ test_copyWriteMSData <- function() {
|
| 185 | 185 |
rt_col <- colnames(hdr_mod) == "retentionTime" |
| 186 | 186 |
checkEquals(hdr_mod[, rt_col], hdr_new[, rt_col], tolerance = 0.01) |
| 187 | 187 |
cn <- colnames(hdr)[!(colnames(hdr) %in% c("injectionTime", "retentionTime",
|
| 188 |
- "filterString", "spectrumId"))] |
|
| 188 |
+ "filterString", "spectrumId", |
|
| 189 |
+ "isolationWindowTargetMZ"))] |
|
| 189 | 190 |
checkEquals(hdr_mod[, cn], hdr_new[, cn]) |
| 190 | 191 |
## checkEquals(ii, ii_new) |
| 191 | 192 |
|
| ... | ... |
@@ -243,7 +244,8 @@ test_copyWriteMSData <- function() {
|
| 243 | 244 |
cn <- colnames(hdr_sub)[!(colnames(hdr_sub) %in% c("injectionTime",
|
| 244 | 245 |
"retentionTime", |
| 245 | 246 |
"filterString", |
| 246 |
- "spectrumId"))] |
|
| 247 |
+ "spectrumId", |
|
| 248 |
+ "isolationWindowTargetMZ"))] |
|
| 247 | 249 |
checkEquals(hdr_sub[, cn], hdr_new[, cn]) |
| 248 | 250 |
|
| 249 | 251 |
## Other mzML: |
| ... | ... |
@@ -441,7 +443,8 @@ test_writeMSData <- function() {
|
| 441 | 443 |
cn <- colnames(hdr_mod)[!(colnames(hdr_mod) %in% c("retentionTime",
|
| 442 | 444 |
"injectionTime", |
| 443 | 445 |
"filterString", |
| 444 |
- "spectrumId"))] |
|
| 446 |
+ "spectrumId", |
|
| 447 |
+ "isolationWindowTargetMZ"))] |
|
| 445 | 448 |
checkEquals(hdr_mod[, cn], hdr_2[, cn]) |
| 446 | 449 |
|
| 447 | 450 |
## Subset. These checks ensure that the scan - precursor scan are mapped |
| ... | ... |
@@ -508,7 +511,8 @@ test_writeMSData <- function() {
|
| 508 | 511 |
cn <- colnames(hdr_sub)[!(colnames(hdr_sub) %in% c("injectionTime",
|
| 509 | 512 |
"retentionTime", |
| 510 | 513 |
"filterString", |
| 511 |
- "spectrumId"))] |
|
| 514 |
+ "spectrumId", |
|
| 515 |
+ "isolationWindowTargetMZ"))] |
|
| 512 | 516 |
checkEquals(hdr_sub[, cn], hdr_new[, cn]) |
| 513 | 517 |
|
| 514 | 518 |
## Other mzML: |
jotsetung authored on 28/03/2018 08:58:15
| ... | ... |
@@ -6,6 +6,14 @@ test_copyWriteMSData <- function() {
|
| 6 | 6 |
## INPUT: mzXML |
| 7 | 7 |
orig_file <- system.file("threonine", "threonine_i2_e35_pH_tree.mzXML",
|
| 8 | 8 |
package = "msdata") |
| 9 |
+ |
|
| 10 |
+ mzML_xsd <- XML::xmlTreeParse(system.file("extdata", "mzML1.1.0.xsd",
|
|
| 11 |
+ package = "mzR"), |
|
| 12 |
+ isSchema = TRUE, useInternal = TRUE) |
|
| 13 |
+ mzML_xsd_idx <- XML::xmlTreeParse(system.file("extdata", "mzML1.1.2_idx.xsd",
|
|
| 14 |
+ package = "mzR"), |
|
| 15 |
+ isSchema = TRUE, useInternal = TRUE) |
|
| 16 |
+ |
|
| 9 | 17 |
mzxml <- openMSfile(orig_file, backend = "pwiz") |
| 10 | 18 |
pks <- peaks(mzxml) |
| 11 | 19 |
hdr <- header(mzxml) |
| ... | ... |
@@ -276,6 +284,17 @@ test_copyWriteMSData <- function() {
|
| 276 | 284 |
} |
| 277 | 285 |
|
| 278 | 286 |
test_writeMSData <- function() {
|
| 287 |
+ mzML_xsd <- XML::xmlTreeParse(system.file("extdata", "mzML1.1.0.xsd",
|
|
| 288 |
+ package = "mzR"), |
|
| 289 |
+ isSchema = TRUE, useInternal = TRUE) |
|
| 290 |
+ mzML_xsd_idx <- XML::xmlTreeParse(system.file("extdata", "mzML1.1.2_idx.xsd",
|
|
| 291 |
+ package = "mzR"), |
|
| 292 |
+ isSchema = TRUE, useInternal = TRUE) |
|
| 293 |
+ mzXML_xsd_idx <- XML::xmlTreeParse(system.file("extdata",
|
|
| 294 |
+ "mzXML_idx_3.2.xsd.xml", |
|
| 295 |
+ package = "mzR"), |
|
| 296 |
+ isSchema = TRUE, useInternal = TRUE) |
|
| 297 |
+ |
|
| 279 | 298 |
test_folder = tempdir() |
| 280 | 299 |
## Input: mzXML |
| 281 | 300 |
test_file <- system.file("threonine", "threonine_i2_e35_pH_tree.mzXML",
|
| ... | ... |
@@ -286,7 +305,7 @@ test_writeMSData <- function() {
|
| 286 | 305 |
mzR::close(in_file) |
| 287 | 306 |
|
| 288 | 307 |
## mzML |
| 289 |
- out_file <- paste0(test_folder, "test_write.mzML") |
|
| 308 |
+ out_file <- paste0(test_folder, "/test_write.mzML") |
|
| 290 | 309 |
writeMSData(file = out_file, header = hdr, object = pks) |
| 291 | 310 |
in_file <- openMSfile(out_file, backend = "pwiz") |
| 292 | 311 |
hdr_2 <- header(in_file) |
| ... | ... |
@@ -295,7 +314,11 @@ test_writeMSData <- function() {
|
| 295 | 314 |
checkEquals(pks, pks_2) |
| 296 | 315 |
checkEquals(peaks(in_file, 13), pks[[13]]) |
| 297 | 316 |
mzR::close(in_file) |
| 298 |
- |
|
| 317 |
+ ## validate mzML: |
|
| 318 |
+ doc <- XML::xmlInternalTreeParse(out_file) |
|
| 319 |
+ res <- XML::xmlSchemaValidate(mzML_xsd_idx, doc) |
|
| 320 |
+ checkEquals(res$status, 0) |
|
| 321 |
+ |
|
| 299 | 322 |
## Test subsetting. |
| 300 | 323 |
hdr_sub <- hdr[c(1, 3, 5), ] |
| 301 | 324 |
hdr_sub$seqNum <- 1:nrow(hdr_sub) |
| ... | ... |
@@ -318,9 +341,13 @@ test_writeMSData <- function() {
|
| 318 | 341 |
hdr_sub_2$spectrumId <- as.integer(factor(hdr_sub_2$spectrumId)) |
| 319 | 342 |
rownames(hdr_sub) <- NULL |
| 320 | 343 |
checkEquals(hdr_sub, hdr_sub_2) |
| 344 |
+ ## validate mzML: |
|
| 345 |
+ doc <- XML::xmlInternalTreeParse(out_file) |
|
| 346 |
+ res <- XML::xmlSchemaValidate(mzML_xsd_idx, doc) |
|
| 347 |
+ checkEquals(res$status, 0) |
|
| 321 | 348 |
|
| 322 | 349 |
## mzXML output: |
| 323 |
- out_file <- paste0(test_folder, "test_write.mzXML") |
|
| 350 |
+ out_file <- paste0(test_folder, "/test_write.mzXML") |
|
| 324 | 351 |
writeMSData(file = out_file, header = hdr, object = pks, |
| 325 | 352 |
outformat = "mzXML") |
| 326 | 353 |
in_file <- openMSfile(out_file, backend = "pwiz") |
| ... | ... |
@@ -351,7 +378,6 @@ test_writeMSData <- function() {
|
| 351 | 378 |
hdr_sub_2$spectrumId <- as.integer(factor(hdr_sub_2$spectrumId)) |
| 352 | 379 |
rownames(hdr_sub) <- NULL |
| 353 | 380 |
checkEquals(hdr_sub, hdr_sub_2) |
| 354 |
- |
|
| 355 | 381 |
|
| 356 | 382 |
## mgf output: |
| 357 | 383 |
## out_file <- paste0(test_folder, "test_write.mgf") |
| ... | ... |
@@ -374,7 +400,7 @@ test_writeMSData <- function() {
|
| 374 | 400 |
mzR::close(in_file) |
| 375 | 401 |
|
| 376 | 402 |
## mzML |
| 377 |
- out_file <- paste0(test_folder, "test_write.mzML") |
|
| 403 |
+ out_file <- paste0(test_folder, "/test_write.mzML") |
|
| 378 | 404 |
writeMSData(pks, file = out_file, header = hdr) |
| 379 | 405 |
in_file <- openMSfile(out_file, backend = "pwiz") |
| 380 | 406 |
hdr_2 <- header(in_file) |
| ... | ... |
@@ -389,9 +415,13 @@ test_writeMSData <- function() {
|
| 389 | 415 |
hdr_2$acquisitionNum <- as.integer(factor(hdr_2$acquisitionNum)) |
| 390 | 416 |
hdr_2$precursorScanNum <- as.integer(factor(hdr_2$precursorScanNum)) |
| 391 | 417 |
checkEquals(hdr_mod, hdr_2) |
| 418 |
+ ## validate mzML: |
|
| 419 |
+ doc <- XML::xmlInternalTreeParse(out_file) |
|
| 420 |
+ res <- XML::xmlSchemaValidate(mzML_xsd_idx, doc) |
|
| 421 |
+ checkEquals(res$status, 0) |
|
| 392 | 422 |
|
| 393 | 423 |
## mzXML output: |
| 394 |
- out_file <- paste0(test_folder, "test_write.mzXML") |
|
| 424 |
+ out_file <- paste0(test_folder, "/test_write.mzXML") |
|
| 395 | 425 |
suppressWarnings( |
| 396 | 426 |
writeMSData(file = out_file, header = hdr, object = pks, |
| 397 | 427 |
outformat = "mzXML") |
| ... | ... |
@@ -489,7 +519,7 @@ test_writeMSData <- function() {
|
| 489 | 519 |
mzR::close(in_file) |
| 490 | 520 |
|
| 491 | 521 |
## mzML |
| 492 |
- out_file <- paste0(test_folder, "test_write.mzML") |
|
| 522 |
+ out_file <- paste0(test_folder, "/test_write.mzML") |
|
| 493 | 523 |
writeMSData(file = out_file, header = hdr, object = pks) |
| 494 | 524 |
in_file <- openMSfile(out_file, backend = "pwiz") |
| 495 | 525 |
hdr_2 <- header(in_file) |
| ... | ... |
@@ -497,6 +527,10 @@ test_writeMSData <- function() {
|
| 497 | 527 |
mzR::close(in_file) |
| 498 | 528 |
checkEquals(hdr, hdr_2) |
| 499 | 529 |
checkEquals(pks, pks_2) |
| 530 |
+ ## validate mzML: |
|
| 531 |
+ doc <- XML::xmlInternalTreeParse(out_file) |
|
| 532 |
+ res <- XML::xmlSchemaValidate(mzML_xsd_idx, doc) |
|
| 533 |
+ checkEquals(res$status, 0) |
|
| 500 | 534 |
|
| 501 | 535 |
## mzXML output: |
| 502 | 536 |
out_file <- paste0(test_folder, "test_write.mzXML") |
| ... | ... |
@@ -518,7 +552,7 @@ test_writeMSData <- function() {
|
| 518 | 552 |
mzR::close(in_file) |
| 519 | 553 |
|
| 520 | 554 |
## mzML |
| 521 |
- out_file <- paste0(test_folder, "test_write.mzML") |
|
| 555 |
+ out_file <- paste0(test_folder, "/test_write.mzML") |
|
| 522 | 556 |
writeMSData(file = out_file, header = hdr, object = pks) |
| 523 | 557 |
in_file <- openMSfile(out_file, backend = "pwiz") |
| 524 | 558 |
hdr_2 <- header(in_file) |
| ... | ... |
@@ -526,6 +560,10 @@ test_writeMSData <- function() {
|
| 526 | 560 |
mzR::close(in_file) |
| 527 | 561 |
checkEquals(hdr, hdr_2) |
| 528 | 562 |
checkEquals(pks, pks_2) |
| 563 |
+ ## validate mzML: |
|
| 564 |
+ doc <- XML::xmlInternalTreeParse(out_file) |
|
| 565 |
+ res <- XML::xmlSchemaValidate(mzML_xsd_idx, doc) |
|
| 566 |
+ checkEquals(res$status, 0) |
|
| 529 | 567 |
|
| 530 | 568 |
## mzXML output: |
| 531 | 569 |
out_file <- paste0(test_folder, "test_write.mzXML") |
- Re-introduce the "MS:-1" CV term for software without CV term, but don't
export this information.
jotsetung authored on 23/03/2018 11:21:05
| ... | ... |
@@ -250,7 +250,7 @@ test_copyWriteMSData <- function() {
|
| 250 | 250 |
out_file <- paste0(test_folder, "test_copyWrite.mzML") |
| 251 | 251 |
mzR::copyWriteMSData(file = out_file, original_file = test_file, |
| 252 | 252 |
header = hdr, object = pks, |
| 253 |
- software_processing = c("MSnbase", "2.3.8"))
|
|
| 253 |
+ software_processing = c("MSnbase", "2.3.8", "MS:-1"))
|
|
| 254 | 254 |
in_file <- openMSfile(out_file, backend = "pwiz") |
| 255 | 255 |
hdr_2 <- header(in_file) |
| 256 | 256 |
pks_2 <- peaks(in_file) |
| ... | ... |
@@ -264,7 +264,7 @@ test_copyWriteMSData <- function() {
|
| 264 | 264 |
out_file <- paste0(test_folder, "test_copyWrite.mzXML") |
| 265 | 265 |
mzR::copyWriteMSData(file = out_file, original_file = test_file, |
| 266 | 266 |
header = hdr, object = pks, outformat = "mzXML", |
| 267 |
- software_processing = c("MSnbase", "2.3.8"))
|
|
| 267 |
+ software_processing = c("MSnbase", "2.3.8", "MS:-1"))
|
|
| 268 | 268 |
in_file <- openMSfile(out_file, backend = "pwiz") |
| 269 | 269 |
hdr_2 <- header(in_file) |
| 270 | 270 |
pks_2 <- peaks(in_file) |
- Read centroiding information from mzML/mzXML files and write it also to these
file types (only supported on pwiz backend).
- ncdf and ramp return centroided=NA.
- Update relevant documentation and unit tests.
jotsetung authored on 23/03/2018 05:37:29
| ... | ... |
@@ -1,9 +1,6 @@ |
| 1 | 1 |
## Testing to write stuff. |
| 2 | 2 |
|
| 3 | 3 |
test_copyWriteMSData <- function() {
|
| 4 |
- library(msdata) |
|
| 5 |
- library(mzR) |
|
| 6 |
- library(RUnit) |
|
| 7 | 4 |
test_folder = tempdir() |
| 8 | 5 |
|
| 9 | 6 |
## INPUT: mzXML |
| ... | ... |
@@ -77,11 +74,12 @@ test_copyWriteMSData <- function() {
|
| 77 | 74 |
mzml_new <- openMSfile(fnew, backend = "pwiz") |
| 78 | 75 |
pks_new <- peaks(mzml_new) |
| 79 | 76 |
hdr_new <- header(mzml_new) |
| 80 |
- mzR::close(mzml_new) |
|
| 81 | 77 |
rownames(hdr_new) <- NULL |
| 82 | 78 |
rownames(hdr_sub) <- NULL |
| 83 | 79 |
checkEquals(pks_new, pks_sub) |
| 84 | 80 |
checkEquals(hdr_new, hdr_sub) |
| 81 |
+ checkEquals(peaks(mzml_new, 2), pks[[3]]) |
|
| 82 |
+ mzR::close(mzml_new) |
|
| 85 | 83 |
## mzXML |
| 86 | 84 |
mzR::copyWriteMSData(file = fnew, original_file = orig_file, |
| 87 | 85 |
header = hdr_sub, object = pks_sub, backend = "pwiz", |
| ... | ... |
@@ -149,11 +147,12 @@ test_copyWriteMSData <- function() {
|
| 149 | 147 |
pks_new <- peaks(mzml_new) |
| 150 | 148 |
hdr_new <- header(mzml_new) |
| 151 | 149 |
ii_new <- mzR::instrumentInfo(mzml_new) |
| 152 |
- mzR::close(mzml_new) |
|
| 153 | 150 |
checkEquals(pks_new, pks) |
| 154 | 151 |
checkEquals(hdr_new, hdr) ## polarity is OK here |
| 155 | 152 |
checkEquals(ii, ii_new) |
| 156 |
- |
|
| 153 |
+ |
|
| 154 |
+ checkEquals(peaks(mzml_new, 12), pks[[12]]) |
|
| 155 |
+ mzR::close(mzml_new) |
|
| 157 | 156 |
## OUTPUT: mzXML |
| 158 | 157 |
fnew <- paste0(test_folder, "test_copyWrite.mzXML") |
| 159 | 158 |
suppressWarnings( |
| ... | ... |
@@ -276,11 +275,7 @@ test_copyWriteMSData <- function() {
|
| 276 | 275 |
checkEquals(ii, ii_2) |
| 277 | 276 |
} |
| 278 | 277 |
|
| 279 |
-test_writeMSData <- function() {
|
|
| 280 |
- |
|
| 281 |
- library(msdata) |
|
| 282 |
- library(mzR) |
|
| 283 |
- library(RUnit) |
|
| 278 |
+test_writeMSData <- function() {
|
|
| 284 | 279 |
test_folder = tempdir() |
| 285 | 280 |
## Input: mzXML |
| 286 | 281 |
test_file <- system.file("threonine", "threonine_i2_e35_pH_tree.mzXML",
|
| ... | ... |
@@ -296,9 +291,10 @@ test_writeMSData <- function() {
|
| 296 | 291 |
in_file <- openMSfile(out_file, backend = "pwiz") |
| 297 | 292 |
hdr_2 <- header(in_file) |
| 298 | 293 |
pks_2 <- peaks(in_file) |
| 299 |
- mzR::close(in_file) |
|
| 300 | 294 |
checkEquals(hdr, hdr_2) |
| 301 | 295 |
checkEquals(pks, pks_2) |
| 296 |
+ checkEquals(peaks(in_file, 13), pks[[13]]) |
|
| 297 |
+ mzR::close(in_file) |
|
| 302 | 298 |
|
| 303 | 299 |
## Test subsetting. |
| 304 | 300 |
hdr_sub <- hdr[c(1, 3, 5), ] |
| ... | ... |
@@ -308,8 +304,9 @@ test_writeMSData <- function() {
|
| 308 | 304 |
in_file <- openMSfile(out_file) |
| 309 | 305 |
hdr_sub_2 <- header(in_file) |
| 310 | 306 |
pks_sub_2 <- peaks(in_file) |
| 311 |
- mzR::close(in_file) |
|
| 312 | 307 |
checkEquals(pks_sub, pks_sub_2) |
| 308 |
+ checkEquals(peaks(in_file, 3), pks[[5]]) |
|
| 309 |
+ mzR::close(in_file) |
|
| 313 | 310 |
## mzXML does not support spectrumId, thus acquisitionNum, precursorScanNum |
| 314 | 311 |
## and spectrumId will be different, but their order and mapping has to be |
| 315 | 312 |
## the same. |
| ... | ... |
@@ -395,8 +392,10 @@ test_writeMSData <- function() {
|
| 395 | 392 |
|
| 396 | 393 |
## mzXML output: |
| 397 | 394 |
out_file <- paste0(test_folder, "test_write.mzXML") |
| 398 |
- writeMSData(file = out_file, header = hdr, object = pks, |
|
| 399 |
- outformat = "mzXML") |
|
| 395 |
+ suppressWarnings( |
|
| 396 |
+ writeMSData(file = out_file, header = hdr, object = pks, |
|
| 397 |
+ outformat = "mzXML") |
|
| 398 |
+ ) |
|
| 400 | 399 |
in_file <- openMSfile(out_file, backend = "pwiz") |
| 401 | 400 |
hdr_2 <- header(in_file) |
| 402 | 401 |
pks_2 <- peaks(in_file) |
| ... | ... |
@@ -456,8 +455,10 @@ test_writeMSData <- function() {
|
| 456 | 455 |
hdr_sub$seqNum <- 1:nrow(hdr_sub) |
| 457 | 456 |
pks_sub <- pks[idx] |
| 458 | 457 |
fnew <- paste0(test_folder, "test_copyWrite.mzXML") |
| 459 |
- writeMSData(file = fnew, header = hdr_sub, object = pks_sub, |
|
| 460 |
- backend = "pwiz", outformat = "mzxml") |
|
| 458 |
+ suppressWarnings( |
|
| 459 |
+ writeMSData(file = fnew, header = hdr_sub, object = pks_sub, |
|
| 460 |
+ backend = "pwiz", outformat = "mzxml") |
|
| 461 |
+ ) |
|
| 461 | 462 |
## Check content is same |
| 462 | 463 |
mzml_new <- openMSfile(fnew, backend = "pwiz") |
| 463 | 464 |
pks_new <- peaks(mzml_new) |
| ... | ... |
@@ -535,5 +536,6 @@ test_writeMSData <- function() {
|
| 535 | 536 |
pks_2 <- peaks(in_file) |
| 536 | 537 |
mzR::close(in_file) |
| 537 | 538 |
checkEquals(pks, pks_2) |
| 539 |
+ hdr$centroided <- FALSE |
|
| 538 | 540 |
checkEquals(hdr, hdr_2) |
| 539 | 541 |
} |
jotsetung authored on 26/02/2018 10:25:18
| ... | ... |
@@ -156,9 +156,11 @@ test_copyWriteMSData <- function() {
|
| 156 | 156 |
|
| 157 | 157 |
## OUTPUT: mzXML |
| 158 | 158 |
fnew <- paste0(test_folder, "test_copyWrite.mzXML") |
| 159 |
- mzR::copyWriteMSData(file = fnew, original_file = orig_file, |
|
| 160 |
- header = hdr, object = pks, backend = "pwiz", |
|
| 161 |
- outformat = "mzxml") |
|
| 159 |
+ suppressWarnings( |
|
| 160 |
+ mzR::copyWriteMSData(file = fnew, original_file = orig_file, |
|
| 161 |
+ header = hdr, object = pks, backend = "pwiz", |
|
| 162 |
+ outformat = "mzxml") |
|
| 163 |
+ ) |
|
| 162 | 164 |
## Check content is same |
| 163 | 165 |
mzml_new <- openMSfile(fnew, backend = "pwiz") |
| 164 | 166 |
pks_new <- peaks(mzml_new) |
| ... | ... |
@@ -211,9 +213,11 @@ test_copyWriteMSData <- function() {
|
| 211 | 213 |
|
| 212 | 214 |
## Subset with mzXML |
| 213 | 215 |
fnew <- paste0(test_folder, "test_copyWrite.mzXML") |
| 214 |
- mzR::copyWriteMSData(file = fnew, original_file = orig_file, |
|
| 215 |
- header = hdr_sub, object = pks_sub, backend = "pwiz", |
|
| 216 |
- outformat = "mzxml") |
|
| 216 |
+ suppressWarnings( |
|
| 217 |
+ mzR::copyWriteMSData(file = fnew, original_file = orig_file, |
|
| 218 |
+ header = hdr_sub, object = pks_sub, backend = "pwiz", |
|
| 219 |
+ outformat = "mzxml") |
|
| 220 |
+ ) |
|
| 217 | 221 |
## Check content is same |
| 218 | 222 |
mzml_new <- openMSfile(fnew, backend = "pwiz") |
| 219 | 223 |
pks_new <- peaks(mzml_new) |
Sebastian Gibb authored on 24/11/2017 11:35:39
| ... | ... |
@@ -176,7 +176,7 @@ test_copyWriteMSData <- function() {
|
| 176 | 176 |
rt_col <- colnames(hdr_mod) == "retentionTime" |
| 177 | 177 |
checkEquals(hdr_mod[, rt_col], hdr_new[, rt_col], tolerance = 0.01) |
| 178 | 178 |
cn <- colnames(hdr)[!(colnames(hdr) %in% c("injectionTime", "retentionTime",
|
| 179 |
- "spectrumId"))] |
|
| 179 |
+ "filterString", "spectrumId"))] |
|
| 180 | 180 |
checkEquals(hdr_mod[, cn], hdr_new[, cn]) |
| 181 | 181 |
## checkEquals(ii, ii_new) |
| 182 | 182 |
|
| ... | ... |
@@ -231,6 +231,7 @@ test_copyWriteMSData <- function() {
|
| 231 | 231 |
checkEquals(hdr_sub[, rt_col], hdr_new[, rt_col], tolerance = 0.01) |
| 232 | 232 |
cn <- colnames(hdr_sub)[!(colnames(hdr_sub) %in% c("injectionTime",
|
| 233 | 233 |
"retentionTime", |
| 234 |
+ "filterString", |
|
| 234 | 235 |
"spectrumId"))] |
| 235 | 236 |
checkEquals(hdr_sub[, cn], hdr_new[, cn]) |
| 236 | 237 |
|
| ... | ... |
@@ -406,6 +407,7 @@ test_writeMSData <- function() {
|
| 406 | 407 |
hdr_2$precursorScanNum <- as.integer(factor(hdr_2$precursorScanNum)) |
| 407 | 408 |
cn <- colnames(hdr_mod)[!(colnames(hdr_mod) %in% c("retentionTime",
|
| 408 | 409 |
"injectionTime", |
| 410 |
+ "filterString", |
|
| 409 | 411 |
"spectrumId"))] |
| 410 | 412 |
checkEquals(hdr_mod[, cn], hdr_2[, cn]) |
| 411 | 413 |
|
| ... | ... |
@@ -470,6 +472,7 @@ test_writeMSData <- function() {
|
| 470 | 472 |
checkEquals(hdr_sub[, rt_col], hdr_new[, rt_col], tolerance = 0.01) |
| 471 | 473 |
cn <- colnames(hdr_sub)[!(colnames(hdr_sub) %in% c("injectionTime",
|
| 472 | 474 |
"retentionTime", |
| 475 |
+ "filterString", |
|
| 473 | 476 |
"spectrumId"))] |
| 474 | 477 |
checkEquals(hdr_sub[, cn], hdr_new[, cn]) |
| 475 | 478 |
|
- Import writeMSData generic from ProtGenerics.
- Convert writeMSData from a function to a method.
jotsetung authored on 20/09/2017 10:19:40
| ... | ... |
@@ -8,7 +8,7 @@ test_copyWriteMSData <- function() {
|
| 8 | 8 |
|
| 9 | 9 |
## INPUT: mzXML |
| 10 | 10 |
orig_file <- system.file("threonine", "threonine_i2_e35_pH_tree.mzXML",
|
| 11 |
- package = "msdata") |
|
| 11 |
+ package = "msdata") |
|
| 12 | 12 |
mzxml <- openMSfile(orig_file, backend = "pwiz") |
| 13 | 13 |
pks <- peaks(mzxml) |
| 14 | 14 |
hdr <- header(mzxml) |
| ... | ... |
@@ -17,8 +17,8 @@ test_copyWriteMSData <- function() {
|
| 17 | 17 |
|
| 18 | 18 |
## OUTPUT: mzML |
| 19 | 19 |
fnew <- paste0(test_folder, "test_copyWrite.mzML") |
| 20 |
- mzR:::copyWriteMSData(filename = fnew, original_file = orig_file, |
|
| 21 |
- header = hdr, data = pks, backend = "pwiz") |
|
| 20 |
+ mzR::copyWriteMSData(file = fnew, original_file = orig_file, |
|
| 21 |
+ header = hdr, object = pks, backend = "pwiz") |
|
| 22 | 22 |
## Check content is same |
| 23 | 23 |
mzml_new <- openMSfile(fnew, backend = "pwiz") |
| 24 | 24 |
pks_new <- peaks(mzml_new) |
| ... | ... |
@@ -31,9 +31,9 @@ test_copyWriteMSData <- function() {
|
| 31 | 31 |
|
| 32 | 32 |
## OUTPUT: mzXML |
| 33 | 33 |
fnew <- paste0(test_folder, "test_copyWrite.mzXML") |
| 34 |
- mzR:::copyWriteMSData(filename = fnew, original_file = orig_file, |
|
| 35 |
- header = hdr, data = pks, backend = "pwiz", |
|
| 36 |
- outformat = "mzxml") |
|
| 34 |
+ mzR::copyWriteMSData(file = fnew, original_file = orig_file, |
|
| 35 |
+ header = hdr, object = pks, backend = "pwiz", |
|
| 36 |
+ outformat = "mzxml") |
|
| 37 | 37 |
## Check content is same |
| 38 | 38 |
mzml_new <- openMSfile(fnew, backend = "pwiz") |
| 39 | 39 |
pks_new <- peaks(mzml_new) |
| ... | ... |
@@ -64,15 +64,15 @@ test_copyWriteMSData <- function() {
|
| 64 | 64 |
pks_sub <- pks[c(1, 3, 5)] |
| 65 | 65 |
fnew <- paste0(test_folder, "test_copyWrite.mzML") |
| 66 | 66 |
## index is not OK after subsetting |
| 67 |
- checkException(mzR:::copyWriteMSData(filename = fnew, |
|
| 67 |
+ checkException(mzR:::copyWriteMSData(file = fnew, |
|
| 68 | 68 |
original_file = orig_file, |
| 69 |
- header = hdr_sub, data = pks_sub, |
|
| 69 |
+ header = hdr_sub, object = pks_sub, |
|
| 70 | 70 |
backend = "pwiz")) |
| 71 | 71 |
hdr_sub$seqNum <- seq_len(nrow(hdr_sub)) |
| 72 | 72 |
## mzML |
| 73 |
- mzR:::copyWriteMSData(filename = fnew, original_file = orig_file, |
|
| 74 |
- header = hdr_sub, data = pks_sub, backend = "pwiz", |
|
| 75 |
- outformat = "mzml") |
|
| 73 |
+ mzR::copyWriteMSData(file = fnew, original_file = orig_file, |
|
| 74 |
+ header = hdr_sub, object = pks_sub, backend = "pwiz", |
|
| 75 |
+ outformat = "mzml") |
|
| 76 | 76 |
## Check content is same |
| 77 | 77 |
mzml_new <- openMSfile(fnew, backend = "pwiz") |
| 78 | 78 |
pks_new <- peaks(mzml_new) |
| ... | ... |
@@ -83,9 +83,9 @@ test_copyWriteMSData <- function() {
|
| 83 | 83 |
checkEquals(pks_new, pks_sub) |
| 84 | 84 |
checkEquals(hdr_new, hdr_sub) |
| 85 | 85 |
## mzXML |
| 86 |
- mzR:::copyWriteMSData(filename = fnew, original_file = orig_file, |
|
| 87 |
- header = hdr_sub, data = pks_sub, backend = "pwiz", |
|
| 88 |
- outformat = "mzxml") |
|
| 86 |
+ mzR::copyWriteMSData(file = fnew, original_file = orig_file, |
|
| 87 |
+ header = hdr_sub, object = pks_sub, backend = "pwiz", |
|
| 88 |
+ outformat = "mzxml") |
|
| 89 | 89 |
## Check content is same |
| 90 | 90 |
mzml_new <- openMSfile(fnew, backend = "pwiz") |
| 91 | 91 |
pks_new <- peaks(mzml_new) |
| ... | ... |
@@ -108,27 +108,27 @@ test_copyWriteMSData <- function() {
|
| 108 | 108 |
## wrong header. |
| 109 | 109 |
## wrong spectra. |
| 110 | 110 |
## wrong data processing. |
| 111 |
- checkException(mzR:::copyWriteMSData(filename = fnew, |
|
| 112 |
- original_file = orig_file, |
|
| 113 |
- header = pks, data = hdr, |
|
| 114 |
- backend = "pwiz")) |
|
| 115 |
- checkException(mzR:::copyWriteMSData(filename = fnew, |
|
| 116 |
- original_file = orig_file, |
|
| 117 |
- header = hdr, data = hdr, |
|
| 118 |
- backend = "pwiz")) |
|
| 119 |
- checkException(mzR:::copyWriteMSData(filename = fnew, |
|
| 120 |
- original_file = orig_file, |
|
| 121 |
- header = hdr, data = pks, |
|
| 122 |
- backend = "Ramp")) |
|
| 123 |
- checkException(mzR:::copyWriteMSData(filename = fnew, |
|
| 124 |
- original_file = "somefile", |
|
| 125 |
- header = hdr, data = pks, |
|
| 126 |
- backend = "pwiz")) |
|
| 127 |
- checkException(mzR:::copyWriteMSData(filename = fnew, |
|
| 128 |
- original_file = orig_file, |
|
| 129 |
- header = hdr, data = pks, |
|
| 130 |
- backend = "pwiz", |
|
| 131 |
- software_processing = c("other")))
|
|
| 111 |
+ checkException(mzR::copyWriteMSData(file = fnew, |
|
| 112 |
+ original_file = orig_file, |
|
| 113 |
+ header = pks, object = hdr, |
|
| 114 |
+ backend = "pwiz")) |
|
| 115 |
+ checkException(mzR::copyWriteMSData(file = fnew, |
|
| 116 |
+ original_file = orig_file, |
|
| 117 |
+ header = hdr, object = hdr, |
|
| 118 |
+ backend = "pwiz")) |
|
| 119 |
+ checkException(mzR::copyWriteMSData(file = fnew, |
|
| 120 |
+ original_file = orig_file, |
|
| 121 |
+ header = hdr, object = pks, |
|
| 122 |
+ backend = "Ramp")) |
|
| 123 |
+ checkException(mzR::copyWriteMSData(file = fnew, |
|
| 124 |
+ original_file = "somefile", |
|
| 125 |
+ header = hdr, object = pks, |
|
| 126 |
+ backend = "pwiz")) |
|
| 127 |
+ checkException(mzR::copyWriteMSData(file = fnew, |
|
| 128 |
+ original_file = orig_file, |
|
| 129 |
+ header = hdr, object = pks, |
|
| 130 |
+ backend = "pwiz", |
|
| 131 |
+ software_processing = c("other")))
|
|
| 132 | 132 |
|
| 133 | 133 |
## INPUT: mzML |
| 134 | 134 |
orig_file <- system.file("proteomics",
|
| ... | ... |
@@ -142,8 +142,8 @@ test_copyWriteMSData <- function() {
|
| 142 | 142 |
|
| 143 | 143 |
## OUTPUT: mzML |
| 144 | 144 |
fnew <- paste0(test_folder, "test_copyWrite.mzML") |
| 145 |
- mzR:::copyWriteMSData(filename = fnew, original_file = orig_file, |
|
| 146 |
- header = hdr, data = pks, backend = "pwiz") |
|
| 145 |
+ mzR::copyWriteMSData(file = fnew, original_file = orig_file, |
|
| 146 |
+ header = hdr, object = pks, backend = "pwiz") |
|
| 147 | 147 |
## Check content is same |
| 148 | 148 |
mzml_new <- openMSfile(fnew, backend = "pwiz") |
| 149 | 149 |
pks_new <- peaks(mzml_new) |
| ... | ... |
@@ -156,9 +156,9 @@ test_copyWriteMSData <- function() {
|
| 156 | 156 |
|
| 157 | 157 |
## OUTPUT: mzXML |
| 158 | 158 |
fnew <- paste0(test_folder, "test_copyWrite.mzXML") |
| 159 |
- mzR:::copyWriteMSData(filename = fnew, original_file = orig_file, |
|
| 160 |
- header = hdr, data = pks, backend = "pwiz", |
|
| 161 |
- outformat = "mzxml") |
|
| 159 |
+ mzR::copyWriteMSData(file = fnew, original_file = orig_file, |
|
| 160 |
+ header = hdr, object = pks, backend = "pwiz", |
|
| 161 |
+ outformat = "mzxml") |
|
| 162 | 162 |
## Check content is same |
| 163 | 163 |
mzml_new <- openMSfile(fnew, backend = "pwiz") |
| 164 | 164 |
pks_new <- peaks(mzml_new) |
| ... | ... |
@@ -194,9 +194,9 @@ test_copyWriteMSData <- function() {
|
| 194 | 194 |
pks_sub <- pks[idx] |
| 195 | 195 |
hdr_sub$seqNum <- 1:nrow(hdr_sub) |
| 196 | 196 |
fnew <- paste0(test_folder, "test_copyWrite.mzML") |
| 197 |
- mzR:::copyWriteMSData(filename = fnew, original_file = orig_file, |
|
| 198 |
- header = hdr_sub, data = pks_sub, backend = "pwiz", |
|
| 199 |
- outformat = "mzml") |
|
| 197 |
+ mzR::copyWriteMSData(file = fnew, original_file = orig_file, |
|
| 198 |
+ header = hdr_sub, object = pks_sub, backend = "pwiz", |
|
| 199 |
+ outformat = "mzml") |
|
| 200 | 200 |
## Check content is same |
| 201 | 201 |
mzml_new <- openMSfile(fnew, backend = "pwiz") |
| 202 | 202 |
pks_new <- peaks(mzml_new) |
| ... | ... |
@@ -211,9 +211,9 @@ test_copyWriteMSData <- function() {
|
| 211 | 211 |
|
| 212 | 212 |
## Subset with mzXML |
| 213 | 213 |
fnew <- paste0(test_folder, "test_copyWrite.mzXML") |
| 214 |
- mzR:::copyWriteMSData(filename = fnew, original_file = orig_file, |
|
| 215 |
- header = hdr_sub, data = pks_sub, backend = "pwiz", |
|
| 216 |
- outformat = "mzxml") |
|
| 214 |
+ mzR::copyWriteMSData(file = fnew, original_file = orig_file, |
|
| 215 |
+ header = hdr_sub, object = pks_sub, backend = "pwiz", |
|
| 216 |
+ outformat = "mzxml") |
|
| 217 | 217 |
## Check content is same |
| 218 | 218 |
mzml_new <- openMSfile(fnew, backend = "pwiz") |
| 219 | 219 |
pks_new <- peaks(mzml_new) |
| ... | ... |
@@ -244,9 +244,9 @@ test_copyWriteMSData <- function() {
|
| 244 | 244 |
|
| 245 | 245 |
## mzML |
| 246 | 246 |
out_file <- paste0(test_folder, "test_copyWrite.mzML") |
| 247 |
- mzR:::copyWriteMSData(filename = out_file, original_file = test_file, |
|
| 248 |
- header = hdr, data = pks, |
|
| 249 |
- software_processing = c("MSnbase", "2.3.8"))
|
|
| 247 |
+ mzR::copyWriteMSData(file = out_file, original_file = test_file, |
|
| 248 |
+ header = hdr, object = pks, |
|
| 249 |
+ software_processing = c("MSnbase", "2.3.8"))
|
|
| 250 | 250 |
in_file <- openMSfile(out_file, backend = "pwiz") |
| 251 | 251 |
hdr_2 <- header(in_file) |
| 252 | 252 |
pks_2 <- peaks(in_file) |
| ... | ... |
@@ -258,9 +258,9 @@ test_copyWriteMSData <- function() {
|
| 258 | 258 |
|
| 259 | 259 |
## mzXML output: |
| 260 | 260 |
out_file <- paste0(test_folder, "test_copyWrite.mzXML") |
| 261 |
- mzR:::copyWriteMSData(filename = out_file, original_file = test_file, |
|
| 262 |
- header = hdr, data = pks, outformat = "mzXML", |
|
| 263 |
- software_processing = c("MSnbase", "2.3.8"))
|
|
| 261 |
+ mzR::copyWriteMSData(file = out_file, original_file = test_file, |
|
| 262 |
+ header = hdr, object = pks, outformat = "mzXML", |
|
| 263 |
+ software_processing = c("MSnbase", "2.3.8"))
|
|
| 264 | 264 |
in_file <- openMSfile(out_file, backend = "pwiz") |
| 265 | 265 |
hdr_2 <- header(in_file) |
| 266 | 266 |
pks_2 <- peaks(in_file) |
| ... | ... |
@@ -287,7 +287,7 @@ test_writeMSData <- function() {
|
| 287 | 287 |
|
| 288 | 288 |
## mzML |
| 289 | 289 |
out_file <- paste0(test_folder, "test_write.mzML") |
| 290 |
- mzR:::writeMSData(filename = out_file, header = hdr, data = pks) |
|
| 290 |
+ writeMSData(file = out_file, header = hdr, object = pks) |
|
| 291 | 291 |
in_file <- openMSfile(out_file, backend = "pwiz") |
| 292 | 292 |
hdr_2 <- header(in_file) |
| 293 | 293 |
pks_2 <- peaks(in_file) |
| ... | ... |
@@ -299,7 +299,7 @@ test_writeMSData <- function() {
|
| 299 | 299 |
hdr_sub <- hdr[c(1, 3, 5), ] |
| 300 | 300 |
hdr_sub$seqNum <- 1:nrow(hdr_sub) |
| 301 | 301 |
pks_sub <- pks[c(1, 3, 5)] |
| 302 |
- mzR:::writeMSData(out_file, header = hdr_sub, data = pks_sub) |
|
| 302 |
+ writeMSData(pks_sub, out_file, header = hdr_sub) |
|
| 303 | 303 |
in_file <- openMSfile(out_file) |
| 304 | 304 |
hdr_sub_2 <- header(in_file) |
| 305 | 305 |
pks_sub_2 <- peaks(in_file) |
| ... | ... |
@@ -319,8 +319,8 @@ test_writeMSData <- function() {
|
| 319 | 319 |
|
| 320 | 320 |
## mzXML output: |
| 321 | 321 |
out_file <- paste0(test_folder, "test_write.mzXML") |
| 322 |
- mzR:::writeMSData(filename = out_file, header = hdr, data = pks, |
|
| 323 |
- outformat = "mzXML") |
|
| 322 |
+ writeMSData(file = out_file, header = hdr, object = pks, |
|
| 323 |
+ outformat = "mzXML") |
|
| 324 | 324 |
in_file <- openMSfile(out_file, backend = "pwiz") |
| 325 | 325 |
hdr_2 <- header(in_file) |
| 326 | 326 |
pks_2 <- peaks(in_file) |
| ... | ... |
@@ -331,8 +331,8 @@ test_writeMSData <- function() {
|
| 331 | 331 |
hdr_sub <- hdr[c(1, 3, 5), ] |
| 332 | 332 |
hdr_sub$seqNum <- 1:nrow(hdr_sub) |
| 333 | 333 |
pks_sub <- pks[c(1, 3, 5)] |
| 334 |
- mzR:::writeMSData(out_file, header = hdr_sub, data = pks_sub, |
|
| 335 |
- outformat = "mzXML") |
|
| 334 |
+ writeMSData(file = out_file, header = hdr_sub, object = pks_sub, |
|
| 335 |
+ outformat = "mzXML") |
|
| 336 | 336 |
in_file <- openMSfile(out_file) |
| 337 | 337 |
hdr_sub_2 <- header(in_file) |
| 338 | 338 |
pks_sub_2 <- peaks(in_file) |
| ... | ... |
@@ -373,7 +373,7 @@ test_writeMSData <- function() {
|
| 373 | 373 |
|
| 374 | 374 |
## mzML |
| 375 | 375 |
out_file <- paste0(test_folder, "test_write.mzML") |
| 376 |
- mzR:::writeMSData(filename = out_file, header = hdr, data = pks) |
|
| 376 |
+ writeMSData(pks, file = out_file, header = hdr) |
|
| 377 | 377 |
in_file <- openMSfile(out_file, backend = "pwiz") |
| 378 | 378 |
hdr_2 <- header(in_file) |
| 379 | 379 |
pks_2 <- peaks(in_file) |
| ... | ... |
@@ -390,8 +390,8 @@ test_writeMSData <- function() {
|
| 390 | 390 |
|
| 391 | 391 |
## mzXML output: |
| 392 | 392 |
out_file <- paste0(test_folder, "test_write.mzXML") |
| 393 |
- mzR:::writeMSData(filename = out_file, header = hdr, data = pks, |
|
| 394 |
- outformat = "mzXML") |
|
| 393 |
+ writeMSData(file = out_file, header = hdr, object = pks, |
|
| 394 |
+ outformat = "mzXML") |
|
| 395 | 395 |
in_file <- openMSfile(out_file, backend = "pwiz") |
| 396 | 396 |
hdr_2 <- header(in_file) |
| 397 | 397 |
pks_2 <- peaks(in_file) |
| ... | ... |
@@ -424,9 +424,9 @@ test_writeMSData <- function() {
|
| 424 | 424 |
hdr_sub$seqNum <- 1:nrow(hdr_sub) |
| 425 | 425 |
pks_sub <- pks[idx] |
| 426 | 426 |
fnew <- paste0(test_folder, "test_copyWrite.mzML") |
| 427 |
- mzR:::writeMSData(filename = fnew, |
|
| 428 |
- header = hdr_sub, data = pks_sub, backend = "pwiz", |
|
| 429 |
- outformat = "mzml") |
|
| 427 |
+ writeMSData(file = fnew, |
|
| 428 |
+ header = hdr_sub, object = pks_sub, backend = "pwiz", |
|
| 429 |
+ outformat = "mzml") |
|
| 430 | 430 |
## Check content is same |
| 431 | 431 |
mzml_new <- openMSfile(fnew, backend = "pwiz") |
| 432 | 432 |
pks_new <- peaks(mzml_new) |
| ... | ... |
@@ -450,8 +450,8 @@ test_writeMSData <- function() {
|
| 450 | 450 |
hdr_sub$seqNum <- 1:nrow(hdr_sub) |
| 451 | 451 |
pks_sub <- pks[idx] |
| 452 | 452 |
fnew <- paste0(test_folder, "test_copyWrite.mzXML") |
| 453 |
- mzR:::writeMSData(filename = fnew, header = hdr_sub, data = pks_sub, |
|
| 454 |
- backend = "pwiz", outformat = "mzxml") |
|
| 453 |
+ writeMSData(file = fnew, header = hdr_sub, object = pks_sub, |
|
| 454 |
+ backend = "pwiz", outformat = "mzxml") |
|
| 455 | 455 |
## Check content is same |
| 456 | 456 |
mzml_new <- openMSfile(fnew, backend = "pwiz") |
| 457 | 457 |
pks_new <- peaks(mzml_new) |
| ... | ... |
@@ -482,7 +482,7 @@ test_writeMSData <- function() {
|
| 482 | 482 |
|
| 483 | 483 |
## mzML |
| 484 | 484 |
out_file <- paste0(test_folder, "test_write.mzML") |
| 485 |
- mzR:::writeMSData(filename = out_file, header = hdr, data = pks) |
|
| 485 |
+ writeMSData(file = out_file, header = hdr, object = pks) |
|
| 486 | 486 |
in_file <- openMSfile(out_file, backend = "pwiz") |
| 487 | 487 |
hdr_2 <- header(in_file) |
| 488 | 488 |
pks_2 <- peaks(in_file) |
| ... | ... |
@@ -492,8 +492,8 @@ test_writeMSData <- function() {
|
| 492 | 492 |
|
| 493 | 493 |
## mzXML output: |
| 494 | 494 |
out_file <- paste0(test_folder, "test_write.mzXML") |
| 495 |
- mzR:::writeMSData(filename = out_file, header = hdr, data = pks, |
|
| 496 |
- outformat = "mzXML") |
|
| 495 |
+ writeMSData(file = out_file, header = hdr, object = pks, |
|
| 496 |
+ outformat = "mzXML") |
|
| 497 | 497 |
in_file <- openMSfile(out_file, backend = "pwiz") |
| 498 | 498 |
hdr_2 <- header(in_file) |
| 499 | 499 |
pks_2 <- peaks(in_file) |
| ... | ... |
@@ -511,7 +511,7 @@ test_writeMSData <- function() {
|
| 511 | 511 |
|
| 512 | 512 |
## mzML |
| 513 | 513 |
out_file <- paste0(test_folder, "test_write.mzML") |
| 514 |
- mzR:::writeMSData(filename = out_file, header = hdr, data = pks) |
|
| 514 |
+ writeMSData(file = out_file, header = hdr, object = pks) |
|
| 515 | 515 |
in_file <- openMSfile(out_file, backend = "pwiz") |
| 516 | 516 |
hdr_2 <- header(in_file) |
| 517 | 517 |
pks_2 <- peaks(in_file) |
| ... | ... |
@@ -521,8 +521,8 @@ test_writeMSData <- function() {
|
| 521 | 521 |
|
| 522 | 522 |
## mzXML output: |
| 523 | 523 |
out_file <- paste0(test_folder, "test_write.mzXML") |
| 524 |
- mzR:::writeMSData(filename = out_file, header = hdr, data = pks, |
|
| 525 |
- outformat = "mzXML") |
|
| 524 |
+ writeMSData(file = out_file, header = hdr, object = pks, |
|
| 525 |
+ outformat = "mzXML") |
|
| 526 | 526 |
in_file <- openMSfile(out_file, backend = "pwiz") |
| 527 | 527 |
hdr_2 <- header(in_file) |
| 528 | 528 |
pks_2 <- peaks(in_file) |
- Read the spectrum ID with the pwiz backend and report the ID in the header
column spectrumId (issue #124).
- Update related documentation and unit tests.
- Fix assignment between spectra and precursor spectra based on the spectrum ID.
jotsetung authored on 07/09/2017 16:09:12
| ... | ... |
@@ -41,7 +41,9 @@ test_copyWriteMSData <- function() {
|
| 41 | 41 |
ii_new <- mzR::instrumentInfo(mzml_new) |
| 42 | 42 |
mzR::close(mzml_new) |
| 43 | 43 |
checkEquals(pks_new, pks) |
| 44 |
- checkEquals(hdr_new, hdr) |
|
| 44 |
+ ## Don't compare IDs since they are different. |
|
| 45 |
+ checkEquals(hdr_new[, colnames(hdr_new) != "spectrumId"], |
|
| 46 |
+ hdr[, colnames(hdr) != "spectrumId"]) |
|
| 45 | 47 |
checkEquals(ii, ii_new) |
| 46 | 48 |