OptiLCMS/NAMESPACE at master · xia-lab/OptiLCMS · GitHub

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
# Generated by roxygen2: do not edit by hand

export(CentroidCheck)
export(CentroidMSData)
export(ExecutePlan)
export(Export.Annotation)
export(Export.PeakSummary)
export(Export.PeakTable)
export(FormatInfusionFeatureTable)
export(FormatMSnAnnotation)
export(FormatPeakList)
export(GaussModel)
export(ImportRawMSData)
export(InitDataObjects)
export(InitializaPlan)
export(PerformBlankSubstraction)
export(PerformDBSearchingBatch)
export(PerformDDADeconvolution)
export(PerformDIADeconvolution)
export(PerformDataInspect)
export(PerformDataTrimming)
export(PerformIndividualInusionFeatureDection)
export(PerformInfusionImport)
export(PerformInusionFeatureDection)
export(PerformMSnImport)
export(PerformMirrorPlotting)
export(PerformParamsOptimization)
export(PerformPeakAlignment)
export(PerformPeakAnnotation)
export(PerformPeakFiling)
export(PerformPeakPicking)
export(PerformPeakProfiling)
export(PerformROIExtraction)
export(PerformResultsExport)
export(PerformSpectrumConsenus)
export(PlotSpectraBPIadj)
export(PlotSpectraInsensityStistics)
export(PlotSpectraPCA)
export(PlotSpectraRTadj)
export(PlotXIC)
export(SetAnnotationParam)
export(SetGlobalParallel)
export(SetPeakParam)
export(SetPlotParam)
export(UpdateRawfiles)
export(plotBPIs)
export(plotMSfeature)
export(plotSingleTIC)
export(plotTICs)
export(running.plan)
export(updateRawSpectraPath)
import(Biobase)
import(BiocParallel)
import(MSnbase)
import(RColorBrewer)
import(ggplot2)
import(methods)
import(parallel)
import(progress)
import(scales)
import(tools)
import(utils)
importFrom(Cairo,Cairo)
importFrom(Cairo,CairoFonts)
importFrom(Hmisc,rcorr)
importFrom(MSnbase,filterMz)
importFrom(RBGL,highlyConnSG)
importFrom(RJSONIO,toJSON)
importFrom(cluster,clusGap)
importFrom(data.table,fwrite)
importFrom(entropy,KL.empirical)
importFrom(ggrepel,geom_text_repel)
importFrom(grDevices,boxplot.stats)
importFrom(grDevices,col2rgb)
importFrom(grDevices,colorRampPalette)
importFrom(grDevices,dev.off)
importFrom(graph,ftM2graphNEL)
importFrom(graphics,boxplot)
importFrom(graphics,grid)
importFrom(graphics,legend)
importFrom(graphics,par)
importFrom(graphics,points)
importFrom(grid,viewport)
importFrom(lattice,cloud)
importFrom(parallel,clusterExport)
importFrom(rsm,ccd)
importFrom(rsm,decode.data)
importFrom(rsm,rsm)
importFrom(stats,approx)
importFrom(stats,approxfun)
importFrom(stats,as.formula)
importFrom(stats,convolve)
importFrom(stats,cor)
importFrom(stats,cor.test)
importFrom(stats,cutree)
importFrom(stats,density)
importFrom(stats,deriv3)
importFrom(stats,dist)
importFrom(stats,dnorm)
importFrom(stats,fft)
importFrom(stats,fitted)
importFrom(stats,getInitial)
importFrom(stats,hclust)
importFrom(stats,kmeans)
importFrom(stats,lm)
importFrom(stats,loess)
importFrom(stats,lsfit)
importFrom(stats,median)
importFrom(stats,model.weights)
importFrom(stats,na.omit)
importFrom(stats,nextn)
importFrom(stats,nls)
importFrom(stats,prcomp)
importFrom(stats,predict)
importFrom(stats,quantile)
importFrom(stats,sd)
importFrom(stats,setNames)
importFrom(stats,smooth.spline)
importFrom(stats,stepfun)
importFrom(stats,var)
importFrom(stats,weighted.mean)
importFrom(tools,file_ext)
importFrom(tools,file_path_as_absolute)
importFrom(utils,head)
importFrom(utils,tail)
useDynLib(OptiLCMS, .registration=TRUE)