From e1ec4ff5d6d730e689e680c87a552d0e1b1f4e1a Mon Sep 17 00:00:00 2001 From: GitHub Actions Date: Thu, 4 Apr 2024 10:47:58 +0000 Subject: [PATCH] cli-14591-2396 --- apple-touch-icon-120x120.png | Bin 9676 -> 9676 bytes apple-touch-icon-152x152.png | Bin 13068 -> 13068 bytes apple-touch-icon-180x180.png | Bin 16269 -> 16269 bytes apple-touch-icon-60x60.png | Bin 4132 -> 4132 bytes apple-touch-icon-76x76.png | Bin 5395 -> 5395 bytes apple-touch-icon.png | Bin 16269 -> 16269 bytes articles/LC-MS-feature-grouping.html | 4 +- articles/index.html | 2 +- articles/xcms-direct-injection.html | 4 +- articles/xcms-lcms-ms.html | 30 +-- articles/xcms.html | 301 ++++++++++++++------------- favicon-16x16.png | Bin 1059 -> 1059 bytes favicon-32x32.png | Bin 2074 -> 2074 bytes pkgdown.yml | 2 +- reference/PlainTextParam.html | 2 +- reference/XCMSnExp-class.html | 2 +- reference/XChromatogram.html | 2 +- reference/applyAdjustedRtime.html | 2 +- reference/chromPeakSpectra.html | 12 +- reference/fillChromPeaks.html | 10 +- search.json | 2 +- 21 files changed, 197 insertions(+), 178 deletions(-) diff --git a/apple-touch-icon-120x120.png b/apple-touch-icon-120x120.png index 8ffcc9d9309953873a172fbdb548db74e18f4ead..d76b813ff2f20e66279929cf83716b3da5b17648 100644 GIT binary patch delta 69 zcmX@(ea3r26$cBKmV)T!>~|ZRrm2XSgcurFnHX6a8)+LDSQ!|^hCi4xSw~eCLqdlu KLSu5QYCZt^UK7j! delta 69 zcmX@(ea3r26$dk~p2qVz98WejO;Zsu4ly*gGBL9q(nX#lga*rSy9**P)F~*9=8WLJSS8OpL6IO|%URtPBk7+OMvgoMR-5A>n^3 KS7`EFqkI4&eHG*Y delta 69 zcmeB4>q(nX#lg(0r#WG^MbXBlYlb4mA%@0QCT3P9hS~-ORt5(8i;iEMoMR-5Arbe# KK6mn5qkI4dA{Gn) diff --git a/apple-touch-icon-180x180.png b/apple-touch-icon-180x180.png index d5df5f68deac0c6bd25332b7503756a620dac2d3..3a73b85e540e63fd643110e0b41aa7a53f0d90c8 100644 GIT binary patch delta 69 zcmeCJ@2#Iu#lga*rQEa2Dr93*xSfbeh@pX%iIJ7DskVWEm4U&G5BH=dzqOOaka)Q^ KZP{cw`+NWoDi%fn delta 69 zcmeCJ@2#Iu#lg(0r^Pub^Tfuca61v>5JO`t6EiClBW(i%D+2>Lue&~z-`dGyNaTyB KewZw0pAP`)j1-*! diff --git a/apple-touch-icon-60x60.png b/apple-touch-icon-60x60.png index 3878a8ad07b2a70535336b85d182e94b071b40aa..dac97f60068d9b5d174d83416d5ac9c4b53b27d6 100644 GIT binary patch delta 93 zcmZ3YutZ@(6$cBKmfV#~Wv&~W-toDbgcurFnHX6a8)zFCSQ!|cI`MHY0|SFRc?MtW?ChKk%5tkt^o+4Y1lp0lX3D^{(Jz58yvg< delta 93 zcmZ3YutZ@(6$dk~o*ILS>f?<~@AzDeLkx|rOw6o|Ewl{`tPBh`{O^`#U|>)!ag8WR iNi0dV%FR#7OsixtGB7gHH2@-X4F?w)FQ2@XKOX=95gTa$ diff --git a/apple-touch-icon-76x76.png b/apple-touch-icon-76x76.png index f5042723f9c910d6cd5b329116c2accd58307d56..210f5988f2d1a5081be0941700c4f6e418fb81d7 100644 GIT binary patch delta 93 zcmbQNHCbyy6$cBKmi*$YZkIPU-4%8<2{AOVGBL6;Hq44S)z;L;6(<;mJ!x@&VHQ8UO$Q diff --git a/apple-touch-icon.png b/apple-touch-icon.png index c3ba5cbf741000452478d0cd00cd55d389757a58..56fd85d497b667e8716e44bff1808605ad262691 100644 GIT binary patch delta 69 zcmeCJ@2#Iu#lga*r6P21{r8Pc;dUY>A%+H4CPr4qX4(b@Rt5$uC62UDerqR-A#uaC K#(J`xeLesrcNNJ1 delta 69 zcmeCJ@2#Iu#lg(0r(HKSGHzp2xSfb`h@r8SiJ6s&v9^JMm4U$y+iO22zqOOakT{u; K=Q3H&J|6%RCKb>C diff --git a/articles/LC-MS-feature-grouping.html b/articles/LC-MS-feature-grouping.html index 0c3edaee..7d38a5ed 100644 --- a/articles/LC-MS-feature-grouping.html +++ b/articles/LC-MS-feature-grouping.html @@ -103,7 +103,7 @@ if (links[i].hostname != window.location.hostname) links[i].target = '_blank'; }); -

Package: xcms
Authors: Johannes Rainer
Modified: 2024-04-03 12:41:11.589186
Compiled: Wed Apr 3 13:49:19 2024

+

Package: xcms
Authors: Johannes Rainer
Modified: 2024-04-04 09:36:23.09377
Compiled: Thu Apr 4 10:45:09 2024

Introduction

@@ -897,7 +897,7 @@

Session information## [91] gtable_0.3.4 sass_0.4.9 ## [93] digest_0.6.35 SparseArray_1.3.4 ## [95] farver_2.1.1 htmlwidgets_1.6.4 -## [97] memoise_2.0.1 htmltools_0.5.8 +## [97] memoise_2.0.1 htmltools_0.5.8.1 ## [99] pkgdown_2.0.7.9000 lifecycle_1.0.4 ## [101] statmod_1.5.0 MASS_7.3-60.2

diff --git a/articles/index.html b/articles/index.html index fa6f1afa..b28a686a 100644 --- a/articles/index.html +++ b/articles/index.html @@ -64,7 +64,7 @@

All vignettes

LC-MS/MS data analysis with xcms
-
LC-MS data pre-processing and analysis with xcms
+
LC-MS data preprocessing and analysis with xcms
diff --git a/articles/xcms-direct-injection.html b/articles/xcms-direct-injection.html index 56b5633e..f59ffba2 100644 --- a/articles/xcms-direct-injection.html +++ b/articles/xcms-direct-injection.html @@ -255,7 +255,7 @@

Correspondence## Number of spectra: 4 ## MSn retention times: -1:59 - -1:59 minutes ## - - - Processing information - - - -## Data loaded [Wed Apr 3 13:50:09 2024] +## Data loaded [Thu Apr 4 10:45:58 2024] ## MSnbase version: 2.29.4 ## - - - Meta data - - - ## phenoData @@ -512,7 +512,7 @@

Session information## [91] pcaMethods_1.95.0 gtable_0.3.4 ## [93] sass_0.4.9 digest_0.6.35 ## [95] SparseArray_1.3.4 htmlwidgets_1.6.4 -## [97] memoise_2.0.1 htmltools_0.5.8 +## [97] memoise_2.0.1 htmltools_0.5.8.1 ## [99] pkgdown_2.0.7.9000 lifecycle_1.0.4 ## [101] statmod_1.5.0 MASS_7.3-60.2 diff --git a/articles/xcms-lcms-ms.html b/articles/xcms-lcms-ms.html index 7c3dc39e..fa39c417 100644 --- a/articles/xcms-lcms-ms.html +++ b/articles/xcms-lcms-ms.html @@ -103,7 +103,7 @@ if (links[i].hostname != window.location.hostname) links[i].target = '_blank'; }); -

Package: xcms
Authors: Johannes Rainer, Michael Witting
Modified: 2024-04-03 12:41:11.589186
Compiled: Wed Apr 3 13:50:18 2024

+

Package: xcms
Authors: Johannes Rainer, Michael Witting
Modified: 2024-04-04 09:36:23.09377
Compiled: Thu Apr 4 10:46:06 2024

Introduction

@@ -267,9 +267,9 @@

Analysis of DDA data## file(s): ## PestMix1_DDA.mzML ## Processing: -## Filter: select retention time [230..610] on MS level(s) 1 2 [Wed Apr 3 13:50:30 2024] -## Filter: select MS level(s) 2 [Wed Apr 3 13:50:37 2024] -## Merge 1 Spectra into one [Wed Apr 3 13:50:37 2024] +## Filter: select retention time [230..610] on MS level(s) 1 2 [Thu Apr 4 10:46:18 2024] +## Filter: select MS level(s) 2 [Thu Apr 4 10:46:26 2024] +## Merge 1 Spectra into one [Thu Apr 4 10:46:26 2024]

By default chromPeakSpectra returns all spectra associated with a MS1 chromatographic peak, but parameter method allows to choose and return only one spectrum per @@ -343,9 +343,9 @@

Analysis of DDA data## file(s): ## PestMix1_DDA.mzML ## Processing: -## Filter: select retention time [230..610] on MS level(s) 1 2 [Wed Apr 3 13:50:30 2024] -## Filter: select MS level(s) 2 [Wed Apr 3 13:50:37 2024] -## Merge 1 Spectra into one [Wed Apr 3 13:50:37 2024] +## Filter: select retention time [230..610] on MS level(s) 1 2 [Thu Apr 4 10:46:18 2024] +## Filter: select MS level(s) 2 [Thu Apr 4 10:46:26 2024] +## Merge 1 Spectra into one [Thu Apr 4 10:46:26 2024]

There are 5 MS2 spectra representing fragmentation of the ion(s) measured in our candidate chromatographic peak. We next reduce this to a single MS2 spectrum using the combineSpectra method @@ -371,9 +371,9 @@

Analysis of DDA data## 1 2 418.926 3505 ## ... 34 more variables/columns. ## Processing: -## Filter: select retention time [230..610] on MS level(s) 1 2 [Wed Apr 3 13:50:30 2024] -## Filter: select MS level(s) 2 [Wed Apr 3 13:50:37 2024] -## Merge 1 Spectra into one [Wed Apr 3 13:50:37 2024] +## Filter: select retention time [230..610] on MS level(s) 1 2 [Thu Apr 4 10:46:18 2024] +## Filter: select MS level(s) 2 [Thu Apr 4 10:46:26 2024] +## Merge 1 Spectra into one [Thu Apr 4 10:46:26 2024] ## ...1 more processings. Use 'processingLog' to list all.

Mass peaks from all input spectra with a difference in m/z smaller 20 ppm (parameter ppm) were combined into one peak and the @@ -832,7 +832,7 @@

Reconstruction of MS2 spectra## CP62 2 574.942 NA ## ... 20 more variables/columns. ## Processing: -## Merge 1 Spectra into one [Wed Apr 3 13:50:45 2024] +## Merge 1 Spectra into one [Thu Apr 4 10:46:33 2024]

As a result we got a Spectra object of length equal to the number of MS1 peaks in our data. The length of a spectrum represents the number of peaks it contains. Thus, a length of 0 indicates that no @@ -994,9 +994,9 @@

Reconstruction of MS2 spectra## file(s): ## PestMix1_DDA.mzML ## Processing: -## Filter: select retention time [230..610] on MS level(s) 1 2 [Wed Apr 3 13:50:30 2024] -## Filter: select MS level(s) 2 [Wed Apr 3 13:50:37 2024] -## Merge 1 Spectra into one [Wed Apr 3 13:50:37 2024] +## Filter: select retention time [230..610] on MS level(s) 1 2 [Thu Apr 4 10:46:18 2024] +## Filter: select MS level(s) 2 [Thu Apr 4 10:46:26 2024] +## Merge 1 Spectra into one [Thu Apr 4 10:46:26 2024]

In total 5 spectra were measured, some with a relatively high number of peaks. Next we combine them into a consensus spectrum.

 diff --git a/articles/xcms.html b/articles/xcms.html index 3ad3d4c0..b288c223 100644 --- a/articles/xcms.html +++ b/articles/xcms.html @@ -6,7 +6,7 @@ -LC-MS data pre-processing and analysis with xcms • xcms +LC-MS data preprocessing and analysis with xcms • xcms @@ -17,7 +17,7 @@ - +