# HG changeset patch # User lecorguille # Date 1453215748 18000 # Node ID 753cde95b6a84f0ce6867426a420ed1df5bbe7b8 # Parent 17d585d877eeb0c731f0e5a9fe3ce89db92ff5a6 Uploaded diff -r 17d585d877ee -r 753cde95b6a8 abims_xcms_report.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/abims_xcms_report.xml Tue Jan 19 10:02:28 2016 -0500 @@ -0,0 +1,69 @@ + + + Create a report of XCMS analysis + + + R + Rscript + xcms + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 10.1093/bioinformatics/btu813 + + + diff -r 17d585d877ee -r 753cde95b6a8 abims_xcms_retcor.xml --- a/abims_xcms_retcor.xml Fri Jan 15 05:06:08 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,301 +0,0 @@ - - - Retention Time Correction using retcor function from xcms R package - - - R - Rscript - xcms - xcms_w4m_script - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - (methods['method'] == 'peakgroups') - (options['option'] == 'show') - (family == 'symmetric') - (plottype != 'none') - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - **xset.group.RData** - -Parameters ----------- - - | Method: -> **peakgroups** - | smooth: -> **loess** - | extra: -> **1** - | missing -> **1** - | Advanced options: -> **show** - | span -> **0.2** - | family -> **gaussian** - | plottype -> **deviation** - - -Output files ------------- - - | **1) xset.group.retcor.RData: RData file** - - | **2) Example of an xset.group.retcor.TICs_corrected pdf file** - -.. image:: xcms_retcor.png - - ]]> - - - 10.1021/ac051437y - 10.1093/bioinformatics/btu813 - - - diff -r 17d585d877ee -r 753cde95b6a8 repository_dependencies.xml --- a/repository_dependencies.xml Fri Jan 15 05:06:08 2016 -0500 +++ b/repository_dependencies.xml Tue Jan 19 10:02:28 2016 -0500 @@ -1,5 +1,4 @@ - - + diff -r 17d585d877ee -r 753cde95b6a8 static/images/xcms_retcor.png Binary file static/images/xcms_retcor.png has changed diff -r 17d585d877ee -r 753cde95b6a8 static/images/xcms_retcor_workflow.png Binary file static/images/xcms_retcor_workflow.png has changed diff -r 17d585d877ee -r 753cde95b6a8 test-data/fillpeaks.RData Binary file test-data/fillpeaks.RData has changed diff -r 17d585d877ee -r 753cde95b6a8 test-data/log.txt --- a/test-data/log.txt Fri Jan 15 05:06:08 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,52 +0,0 @@ - PACKAGE INFO -parallel 3.1.2 -BiocGenerics 0.14.0 -Biobase 2.28.0 -Rcpp 0.12.0 -mzR 2.2.2 -xcms 1.44.0 -snow 0.3.13 -batch 1.1.4 - - - ARGUMENTS INFO -image test-data/xset.group.RData -xfunction retcor -xsetRdataOutput test-data/xset.group.retcor.RData -ticspdf xset.group.retcor.TICs_corrected.pdf -bicspdf xset.group.retcor.BPCs_corrected.pdf -rplotspdf xset.group.retcor.Rplots.pdf -method obiwarp -profStep 1 -zipfile test-data/sacuri.zip - - - INFILE PROCESSING INFO - - - ARGUMENTS PROCESSING INFO - - - MAIN PROCESSING INFO -center sample: HU_neg_060 -Processing: HU_neg_028 HU_neg_051 HU_neg_017 HU_neg_034 Blanc09 Blanc06 Blanc12 Blanc04 -null device - 1 - - - XSET OBJECT INFO -An "xcmsSet" object with 9 samples - -Time range: 0.7-1139.9 seconds (0-19 minutes) -Mass range: 50.0019-999.9863 m/z -Peaks: 135846 (about 15094 per sample) -Peak Groups: 0 -Sample classes: bio, blank - -Profile settings: method = bin - step = 0.01 - -Memory usage: 13.8 MB - - - DONE diff -r 17d585d877ee -r 753cde95b6a8 test-data/report.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/report.html Tue Jan 19 10:02:28 2016 -0500 @@ -0,0 +1,74 @@ + + + + +[W4M] XCMS analysis report + + + +

___ XCMS analysis report using Workflow4Metabolomics ___

+

Samples used:

+ + +
samplefilename
HU_neg_051 sacuri//bio2/HU_neg_051.mzXML
HU_neg_060 sacuri//bio2/HU_neg_060.mzXML
HU_neg_017 sacuri//bio/HU_neg_017.mzXML
HU_neg_028 sacuri//bio/HU_neg_028.mzXML
Blanc04 sacuri//blank/Blanc04.mzXML
Blanc06 sacuri//blank/Blanc06.mzXML
+

Function launched:

+ + + + + + + + + + + + + + + +
timestamp
(ymd-h:m:s)		functionargumentvalue
151221-16:20:54xcmsSetnSlaves1
methodmatchedFilter
step0.01
fwhm30
151221-16:37:00groupmethoddensity
sleep0.001
minfrac0.5
bw30
mzwid0.25
151221-16:37:20fillPeaksmethodchrom
+

Information about the xcmsSet object:

+
+An "xcmsSet" object with 6 samples
+
+Time range: 16.3-1138.9 seconds (0.3-19 minutes)
+Mass range: 61.9883-481.2446 m/z
+Peaks: 1799 (about 300 per sample)
+Peak Groups: 289 
+Sample classes: bio, bio2, blank 
+
+Profile settings: method = bin
+                  step = 0.01
+
+Memory usage: 0.421 MB
+
+

Citations:

+ + + diff -r 17d585d877ee -r 753cde95b6a8 test-data/sacuri.zip Binary file test-data/sacuri.zip has changed diff -r 17d585d877ee -r 753cde95b6a8 test-data/xset.group.RData Binary file test-data/xset.group.RData has changed diff -r 17d585d877ee -r 753cde95b6a8 test-data/xset.group.retcor.BPCs_corrected.pdf Binary file test-data/xset.group.retcor.BPCs_corrected.pdf has changed diff -r 17d585d877ee -r 753cde95b6a8 test-data/xset.group.retcor.RData Binary file test-data/xset.group.retcor.RData has changed diff -r 17d585d877ee -r 753cde95b6a8 test-data/xset.group.retcor.Rplots.pdf Binary file test-data/xset.group.retcor.Rplots.pdf has changed diff -r 17d585d877ee -r 753cde95b6a8 test-data/xset.group.retcor.TICs_corrected.pdf Binary file test-data/xset.group.retcor.TICs_corrected.pdf has changed