1. omicRexposome
  2. NAMESPACE
Browse code

Updated SVA

Now "association" implements isva (fast) and sva pipelines (slow).

Vignette was updated.
Doc. was updated.

Carles Hernandez-Ferrer authored on 28/09/2017 12:22:39
Showing 1 changed files
NAMESPACE
History View file @ ba75623
... ... 
@@ -54,6 +54,7 @@ importFrom(stats,model.matrix)
54 54 
 importFrom(stats,qbeta)
55 55 
 importFrom(stats,qchisq)
56 56 
 importFrom(stats,qnorm)
57 
+importFrom(stats,relevel)
57 58 
 importFrom(stringr,str_pad)
58 59 
 importFrom(sva,num.sv)
59 60 
 importFrom(sva,sva)
Browse code

solved bug when null model selected for association.

carleshf authored on 19/08/2017 21:40:49
Showing 1 changed files
NAMESPACE
History View file @ ce17dbd
... ... 
@@ -47,7 +47,6 @@ importFrom(limma,lmFit)
47 47 
 importFrom(methods,as)
48 48 
 importFrom(methods,new)
49 49 
 importFrom(omicade4,mcia)
50 
-importFrom(qqman,manhattan)
51 50 
 importFrom(rexposome,exposureNames)
52 51 
 importFrom(rexposome,phenotypeNames)
53 52 
 importFrom(stats,as.formula)
Browse code

Updated omicRexposome - documentation, examples and checking.

carleshf authored on 17/07/2017 12:43:58
Showing 1 changed files
NAMESPACE
History View file @ 8f7f675
... ... 
@@ -4,6 +4,7 @@ export(add_cls)
4 4 
 export(add_exp)
5 5 
 export(association)
6 6 
 export(crossomics)
7 
+export(getIntegration)
7 8 
 export(plotAssociation)
8 9 
 export(plotHits)
9 10 
 export(plotIntegration)
... ... 
@@ -22,6 +23,10 @@ importFrom(Biobase,sampleNames)
22 23 
 importFrom(MultiDataSet,commonSamples)
23 24 
 importFrom(PMA,MultiCCA)
24 25 
 importFrom(PMA,MultiCCA.permute)
26 
+importFrom(SmartSVA,smartsva.cpp)
27 
+importFrom(SummarizedExperiment,assay)
28 
+importFrom(SummarizedExperiment,rowData)
29 
+importFrom(SummarizedExperiment,rowRanges)
25 30 
 importFrom(ggplot2,aes)
26 31 
 importFrom(ggplot2,geom_hline)
27 32 
 importFrom(ggplot2,geom_point)
... ... 
@@ -36,6 +41,7 @@ importFrom(ggrepel,geom_text_repel)
36 41 
 importFrom(grDevices,rainbow)
37 42 
 importFrom(graphics,plot)
38 43 
 importFrom(gridExtra,grid.arrange)
44 
+importFrom(isva,EstDimRMT)
39 45 
 importFrom(limma,eBayes)
40 46 
 importFrom(limma,lmFit)
41 47 
 importFrom(methods,as)
... ... 
@@ -49,5 +55,6 @@ importFrom(stats,model.matrix)
49 55 
 importFrom(stats,qbeta)
50 56 
 importFrom(stats,qchisq)
51 57 
 importFrom(stats,qnorm)
58 
+importFrom(stringr,str_pad)
52 59 
 importFrom(sva,num.sv)
53 60 
 importFrom(sva,sva)
Browse code

Solved bug in plotAssociation. Updated vignette. Solved problems in corssomics. Readjusted tableHits, table Lambda, plotHits and plotLambda.

carleshf authored on 11/07/2017 16:48:33
Showing 1 changed files
NAMESPACE
History View file @ 9c166cd
... ... 
@@ -4,6 +4,7 @@ export(add_cls)
4 4 
 export(add_exp)
5 5 
 export(association)
6 6 
 export(crossomics)
7 
+export(plotAssociation)
7 8 
 export(plotHits)
8 9 
 export(plotIntegration)
9 10 
 export(plotLambda)
Browse code

ResultSet moved to MultiDataSet. Updated from sva to SmartSVA. MEthylation pipeline needs test.

carleshf authored on 21/06/2017 08:00:33
Showing 1 changed files
NAMESPACE
History View file @ 079c1ec
... ... 
@@ -4,21 +4,15 @@ export(add_cls)
4 4 
 export(add_exp)
5 5 
 export(association)
6 6 
 export(crossomics)
7 
-export(lambdaClayton)
8 
-export(opt)
9 
-export(plotAssociation)
10 7 
 export(plotHits)
11 8 
 export(plotIntegration)
12 9 
 export(plotLambda)
13 
-export(qq_plot)
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-export(rid)
15 10 
 export(tableHits)
16 11 
 export(tableLambda)
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-export(topTable)
18 
-exportClasses(ResultSet)
19 12 
 import(methods)
20 13 
 import(utils)
21 14 
 importClassesFrom(MultiDataSet,MultiDataSet)
15 
+importClassesFrom(MultiDataSet,ResultSet)
22 16 
 importClassesFrom(rexposome,ExposomeClust)
23 17 
 importClassesFrom(rexposome,ExposomeSet)
24 18 
 importFrom(Biobase,fData)
Browse code

General update of 'omicRexposome', included 'MultiDataSet'. Created 'association'. 'crossomics' needs upate and validation.

kuragari authored on 16/06/2017 15:52:39
Showing 1 changed files
NAMESPACE
History View file @ 4ef8eca
... ... 
@@ -2,7 +2,6 @@
2 2
3 3 
 export(add_cls)
4 4 
 export(add_exp)
5 
-export(assocES)
6 5 
 export(association)
7 6 
 export(crossomics)
8 7 
 export(lambdaClayton)
Browse code

Added 'association' method for 'MultiDataSet' objects.

Carles Hernandez-Ferrer authored on 14/06/2017 10:58:27
Showing 1 changed files
NAMESPACE
History View file @ c058ce7
... ... 
@@ -1,6 +1,9 @@
1 1 
 # Generated by roxygen2: do not edit by hand
2 2
3 
+export(add_cls)
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+export(add_exp)
3 5 
 export(assocES)
6 
+export(association)
4 7 
 export(crossomics)
5 8 
 export(lambdaClayton)
6 9 
 export(opt)
... ... 
@@ -13,15 +16,16 @@ export(rid)
13 16 
 export(tableHits)
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 export(tableLambda)
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 export(topTable)
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-export(volcano_plot)
17 19 
 exportClasses(ResultSet)
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 import(methods)
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 import(utils)
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+importClassesFrom(MultiDataSet,MultiDataSet)
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 importClassesFrom(rexposome,ExposomeClust)
21 24 
 importClassesFrom(rexposome,ExposomeSet)
22 25 
 importFrom(Biobase,fData)
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 importFrom(Biobase,pData)
24 27 
 importFrom(Biobase,sampleNames)
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+importFrom(MultiDataSet,commonSamples)
25 29 
 importFrom(PMA,MultiCCA)
26 30 
 importFrom(PMA,MultiCCA.permute)
27 31 
 importFrom(ggplot2,aes)
Browse code

Full update of NAMESPACE

Properly generation of 'NAMESPACE' using 'omicRexposome.R' file.

Carles Hernandez-Ferrer authored on 19/04/2017 19:23:19
Showing 1 changed files
NAMESPACE
History View file @ 4ef2ed4
... ... 
@@ -10,9 +10,46 @@ export(plotIntegration)
10 10 
 export(plotLambda)
11 11 
 export(qq_plot)
12 12 
 export(rid)
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-export(snpToContinuous)
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 export(tableHits)
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 export(tableLambda)
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 export(topTable)
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 export(volcano_plot)
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 exportClasses(ResultSet)
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+import(methods)
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+import(utils)
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+importClassesFrom(rexposome,ExposomeClust)
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+importClassesFrom(rexposome,ExposomeSet)
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+importFrom(Biobase,fData)
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+importFrom(Biobase,pData)
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+importFrom(Biobase,sampleNames)
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+importFrom(PMA,MultiCCA)
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+importFrom(PMA,MultiCCA.permute)
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+importFrom(ggplot2,aes)
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+importFrom(ggplot2,geom_hline)
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+importFrom(ggplot2,geom_point)
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+importFrom(ggplot2,geom_polygon)
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+importFrom(ggplot2,geom_vline)
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+importFrom(ggplot2,scale_colour_manual)
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+importFrom(ggplot2,theme)
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+importFrom(ggplot2,theme_bw)
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+importFrom(ggplot2,xlab)
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+importFrom(ggplot2,ylab)
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+importFrom(ggrepel,geom_text_repel)
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+importFrom(grDevices,rainbow)
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+importFrom(graphics,plot)
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+importFrom(gridExtra,grid.arrange)
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+importFrom(limma,eBayes)
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+importFrom(limma,lmFit)
43 
+importFrom(methods,as)
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+importFrom(methods,new)
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+importFrom(omicade4,mcia)
46 
+importFrom(qqman,manhattan)
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+importFrom(rexposome,exposureNames)
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+importFrom(rexposome,phenotypeNames)
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+importFrom(stats,as.formula)
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+importFrom(stats,model.matrix)
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+importFrom(stats,qbeta)
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+importFrom(stats,qchisq)
53 
+importFrom(stats,qnorm)
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+importFrom(sva,num.sv)
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+importFrom(sva,sva)
Browse code

Updated documentation - added examples. Updated vignette.

carleshf authored on 31/03/2017 14:49:44
Showing 1 changed files
NAMESPACE
History View file @ 60f5190
... ... 
@@ -3,7 +3,7 @@
3 3 
 export(assocES)
4 4 
 export(crossomics)
5 5 
 export(lambdaClayton)
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-export(options)
6 
+export(opt)
7 7 
 export(plotAssociation)
8 8 
 export(plotHits)
9 9 
 export(plotIntegration)
Browse code

Removed 'MultiDataSet' methods. Updated 'crossomics' with 'MultiCCA' from 'PMA'. Updated 'plotIntegration'.

carleshf authored on 28/03/2017 23:30:19
Showing 1 changed files
NAMESPACE
History View file @ d6d5744
... ... 
@@ -3,6 +3,7 @@
3 3 
 export(assocES)
4 4 
 export(crossomics)
5 5 
 export(lambdaClayton)
6 
+export(options)
6 7 
 export(plotAssociation)
7 8 
 export(plotHits)
8 9 
 export(plotIntegration)
Browse code

'crossomics' function using 'MultiCCA' method from 'PMA' is working.

carleshf authored on 28/03/2017 21:12:28
Showing 1 changed files
NAMESPACE
History View file @ a135a43
... ... 
@@ -1,6 +1,7 @@
1 1 
 # Generated by roxygen2: do not edit by hand
2 2
3 3 
 export(assocES)
4 
+export(crossomics)
4 5 
 export(lambdaClayton)
5 6 
 export(plotAssociation)
6 7 
 export(plotHits)
Browse code

Created 'assocES'

Created new function 'assocES' to use without 'MultiDataSet'.

carleshf authored on 26/03/2017 21:11:03
Showing 1 changed files
NAMESPACE
History View file @ bcaff11
... ... 
@@ -1,17 +1,11 @@
1 1 
 # Generated by roxygen2: do not edit by hand
2 2
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-export(add_cls)
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-export(add_exp)
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-export(add_prot)
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-export(assocGE)
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-export(assocME)
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-export(assocPRT)
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-export(assocSNP)
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-export(crossomics)
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+export(assocES)
11 4 
 export(lambdaClayton)
12 5 
 export(plotAssociation)
13 6 
 export(plotHits)
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 export(plotIntegration)
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+export(plotLambda)
15 9 
 export(qq_plot)
16 10 
 export(rid)
17 11 
 export(snpToContinuous)
... ... 
@@ -20,4 +14,3 @@ export(tableLambda)
20 14 
 export(topTable)
21 15 
 export(volcano_plot)
22 16 
 exportClasses(ResultSet)
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-importClassesFrom(MultiDataSet,MethylationSet)
Browse code

Updated 'corssomics'.

carleshf authored on 26/03/2017 17:06:17
Showing 1 changed files
NAMESPACE
History View file @ 026c7b9
... ... 
@@ -7,9 +7,11 @@ export(assocGE)
7 7 
 export(assocME)
8 8 
 export(assocPRT)
9 9 
 export(assocSNP)
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+export(crossomics)
10 11 
 export(lambdaClayton)
11 12 
 export(plotAssociation)
12 13 
 export(plotHits)
14 
+export(plotIntegration)
13 15 
 export(qq_plot)
14 16 
 export(rid)
15 17 
 export(snpToContinuous)
Browse code

Added methods to 'MultiDataSet'

Added both 'add_exp' and 'add_cls' for 'MultiDataSet'.

carleshf authored on 24/03/2017 14:13:35
Showing 1 changed files
NAMESPACE
History View file @ d2a7f42
... ... 
@@ -1,10 +1,13 @@
1 1 
 # Generated by roxygen2: do not edit by hand
2 2
3 
+export(add_cls)
4 
+export(add_exp)
3 5 
 export(add_prot)
4 6 
 export(assocGE)
5 7 
 export(assocME)
6 8 
 export(assocPRT)
7 9 
 export(assocSNP)
10 
+export(lambdaClayton)
8 11 
 export(plotAssociation)
9 12 
 export(plotHits)
10 13 
 export(qq_plot)
Browse code

Export 'topTable'.

carleshf authored on 19/03/2017 15:37:14
Showing 1 changed files
NAMESPACE
History View file @ 33dd09f
... ... 
@@ -12,6 +12,7 @@ export(rid)
12 12 
 export(snpToContinuous)
13 13 
 export(tableHits)
14 14 
 export(tableLambda)
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+export(topTable)
15 16 
 export(volcano_plot)
16 17 
 exportClasses(ResultSet)
17 18 
 importClassesFrom(MultiDataSet,MethylationSet)
Browse code

reorganization - needs more work

Carles Hernandez-Ferrer authored on 17/03/2017 17:16:34
Showing 1 changed files
NAMESPACE
History View file @ 004d3ba
... ... 
@@ -1,73 +1,17 @@
1 1 
 # Generated by roxygen2: do not edit by hand
2 2
3 
-export("individualNames<-")
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-export(Summary)
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-export(add_cls)
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-export(add_exp)
7 3 
 export(add_prot)
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-export(as.data.frame.ExposomeSet)
9 4 
 export(assocGE)
10 5 
 export(assocME)
11 6 
 export(assocPRT)
12 7 
 export(assocSNP)
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-export(classification)
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-export(clustering)
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-export(correlation)
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-export(crossomics)
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-export(expos)
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-export(exposureNames)
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-export(extract)
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-export(exwas)
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-export(familyNames)
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-export(highAndLow)
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-export(ilod)
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-export(impute)
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-export(imputeLOD)
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-export(individualNames)
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-export(lambdaClayton)
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-export(load_exposome)
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-export(mexwas)
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-export(ndim)
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-export(nl_exwas)
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-export(normalityTest)
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-export(pca)
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-export(phenotypeNames)
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-export(plot3PCA)
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 export(plotAssociation)
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-export(plotClassification)
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-export(plotCorrelation)
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-export(plotEXP)
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-export(plotEffect)
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-export(plotExwas)
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-export(plotFamily)
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-export(plotHistogram)
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 export(plotHits)
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-export(plotIntegration)
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-export(plotLOD)
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-export(plotMissings)
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-export(plotPCA)
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-export(plotPHE)
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 export(qq_plot)
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-export(raw)
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-export(read_exposome)
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-export(restore)
54 11 
 export(rid)
55 12 
 export(snpToContinuous)
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-export(standardize)
57 13 
 export(tableHits)
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-export(tableLOD)
59 14 
 export(tableLambda)
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-export(tableMissings)
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-export(tef)
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-export(trans)
63 15 
 export(volcano_plot)
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-exportClasses(ExWAS)
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-exportClasses(ExposomeClust)
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-exportClasses(ExposomeCorr)
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-exportClasses(ExposomePCA)
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-exportClasses(ExposomeSet)
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 exportClasses(ResultSet)
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-exportClasses(mExWAS)
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-exportClasses(nlExWAS)
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-importClassesFrom(Biobase,eSet)
73 17 
 importClassesFrom(MultiDataSet,MethylationSet)
Browse code

First commit after restructuration.

carleshf authored on 09/03/2017 17:17:22
Showing 1 changed files
NAMESPACE
History View file @ 50422aa
1 1 
new file mode 100644
... ... 
@@ -0,0 +1,73 @@
1 
+# Generated by roxygen2: do not edit by hand
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+
3 
+export("individualNames<-")
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+export(Summary)
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+export(add_cls)
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+export(add_exp)
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+export(add_prot)
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+export(as.data.frame.ExposomeSet)
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+export(assocGE)
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+export(assocME)
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+export(assocPRT)
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+export(assocSNP)
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+export(classification)
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+export(clustering)
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+export(correlation)
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+export(crossomics)
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+export(expos)
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+export(exposureNames)
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+export(extract)
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+export(exwas)
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+export(familyNames)
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+export(highAndLow)
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+export(ilod)
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+export(impute)
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+export(imputeLOD)
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+export(individualNames)
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+export(lambdaClayton)
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+export(load_exposome)
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+export(mexwas)
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+export(ndim)
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+export(nl_exwas)
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+export(normalityTest)
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+export(pca)
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+export(phenotypeNames)
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+export(plot3PCA)
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+export(plotAssociation)
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+export(plotClassification)
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+export(plotCorrelation)
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+export(plotEXP)
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+export(plotEffect)
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+export(plotExwas)
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+export(plotFamily)
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+export(plotHistogram)
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+export(plotHits)
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+export(plotIntegration)
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+export(plotLOD)
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+export(plotMissings)
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+export(plotPCA)
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+export(plotPHE)
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+export(qq_plot)
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+export(raw)
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+export(read_exposome)
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+export(restore)
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+export(rid)
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+export(snpToContinuous)
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+export(standardize)
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+export(tableHits)
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+export(tableLOD)
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+export(tableLambda)
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+export(tableMissings)
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+export(tef)
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+export(trans)
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+export(volcano_plot)
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+exportClasses(ExWAS)
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+exportClasses(ExposomeClust)
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+exportClasses(ExposomeCorr)
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+exportClasses(ExposomePCA)
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+exportClasses(ExposomeSet)
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+exportClasses(ResultSet)
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+exportClasses(mExWAS)
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+exportClasses(nlExWAS)
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+importClassesFrom(Biobase,eSet)
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+importClassesFrom(MultiDataSet,MethylationSet)