1. TPP2D
  2. NAMESPACE
Browse code

added new function for faster fstat null distribution estimation and bumped version

Nils Kurzawa authored on 24/11/2022 13:09:07
Showing 1 changed files
NAMESPACE
History View file @ 8b5ab49
... ... 
@@ -4,6 +4,7 @@ export(TPP_importCheckConfigTable)
4 4 
 export(annotateDataList)
5 5 
 export(bootstrapNull)
6 6 
 export(bootstrapNullAlternativeModel)
7 
+export(bootstrapNullAlternativeModelFast)
7 8 
 export(competeModels)
8 9 
 export(computeFStatFromParams)
9 10 
 export(computeFstat)
Browse code

added volcano plot function, small fix in FDR function, extended vignette

Nils Kurzawa authored on 19/06/2020 15:49:26
Showing 1 changed files
NAMESPACE
History View file @ 3fab3a9
... ... 
@@ -24,6 +24,7 @@ export(plot2dTppFcHeatmap)
24 24 
 export(plot2dTppFit)
25 25 
 export(plot2dTppProfile)
26 26 
 export(plot2dTppRelProfile)
27 
+export(plot2dTppVolcano)
27 28 
 export(recomputeSignalFromRatios)
28 29 
 export(renameColumns)
29 30 
 export(resolveAmbiguousProteinNames)
Browse code

added plotting function for heatmap visualization

Nils Kurzawa authored on 17/06/2020 14:59:50
Showing 1 changed files
NAMESPACE
History View file @ 7115034
... ... 
@@ -20,6 +20,7 @@ export(getPvalues)
20 20 
 export(gg_qq)
21 21 
 export(import2dDataset)
22 22 
 export(import2dMain)
23 
+export(plot2dTppFcHeatmap)
23 24 
 export(plot2dTppFit)
24 25 
 export(plot2dTppProfile)
25 26 
 export(plot2dTppRelProfile)
Browse code

finalized defuncing computeFdr

Nils Kurzawa authored on 16/06/2020 14:32:29
Showing 1 changed files
NAMESPACE
History View file @ 14cc378
... ... 
@@ -6,7 +6,6 @@ export(bootstrapNull)
6 6 
 export(bootstrapNullAlternativeModel)
7 7 
 export(competeModels)
8 8 
 export(computeFStatFromParams)
9 
-export(computeFdr)
10 9 
 export(computeFstat)
11 10 
 export(configWide2Long)
12 11 
 export(filterOutContaminants)
Browse code

added option to shrink F stat denominator using limma::squeezeVar

Nils Kurzawa authored on 09/04/2020 08:24:10
Showing 1 changed files
NAMESPACE
History View file @ 045c02d
... ... 
@@ -37,6 +37,7 @@ importFrom(RCurl,url.exists)
37 37 
 importFrom(doParallel,registerDoParallel)
38 38 
 importFrom(foreach,"%dopar%")
39 39 
 importFrom(foreach,foreach)
40 
+importFrom(limma,squeezeVar)
40 41 
 importFrom(methods,is)
41 42 
 importFrom(methods,new)
42 43 
 importFrom(openxlsx,read.xlsx)
Browse code

added function to compute pEC50 at specified temperature for protein of interest

Nils Kurzawa authored on 30/03/2020 15:32:18
Showing 1 changed files
NAMESPACE
History View file @ 3f0cb5e
... ... 
@@ -16,6 +16,7 @@ export(fitH0Model)
16 16 
 export(fitH1Model)
17 17 
 export(getFDR)
18 18 
 export(getModelParamsDf)
19 
+export(getPEC504Temperature)
19 20 
 export(getPvalues)
20 21 
 export(gg_qq)
21 22 
 export(import2dDataset)
Browse code

replaced function for computing p-values

Nils Kurzawa authored on 29/01/2020 09:21:15
Showing 1 changed files
NAMESPACE
History View file @ 08e4232
... ... 
@@ -8,7 +8,6 @@ export(competeModels)
8 8 
 export(computeFStatFromParams)
9 9 
 export(computeFdr)
10 10 
 export(computeFstat)
11 
-export(computePvalFromKernelDensity)
12 11 
 export(configWide2Long)
13 12 
 export(filterOutContaminants)
14 13 
 export(findHits)
... ... 
@@ -42,7 +41,6 @@ importFrom(methods,new)
42 41 
 importFrom(openxlsx,read.xlsx)
43 42 
 importFrom(parallel,makeCluster)
44 43 
 importFrom(parallel,stopCluster)
45 
-importFrom(sfsmisc,integrate.xy)
46 44 
 importFrom(stats,approx)
47 45 
 importFrom(stats,coef)
48 46 
 importFrom(stats,density)
Browse code

added new function for computing p-values to replace kernel density-based one, added missing documentation for gg_qq plot parameter

Nils Kurzawa authored on 29/01/2020 09:03:26
Showing 1 changed files
NAMESPACE
History View file @ ced496d
... ... 
@@ -17,6 +17,7 @@ export(fitH0Model)
17 17 
 export(fitH1Model)
18 18 
 export(getFDR)
19 19 
 export(getModelParamsDf)
20 
+export(getPvalues)
20 21 
 export(gg_qq)
21 22 
 export(import2dDataset)
22 23 
 export(import2dMain)
Browse code

fixed typo in function name: resolveAmbigUousProteinNames

Nils Kurzawa authored on 26/01/2020 14:37:31
Showing 1 changed files
NAMESPACE
History View file @ 12a8881
... ... 
@@ -25,7 +25,7 @@ export(plot2dTppProfile)
25 25 
 export(plot2dTppRelProfile)
26 26 
 export(recomputeSignalFromRatios)
27 27 
 export(renameColumns)
28 
-export(resolveAmbigousProteinNames)
28 
+export(resolveAmbiguousProteinNames)
29 29 
 export(runTPP2D)
30 30 
 exportClasses(tpp2dExperiment)
31 31 
 import(BiocParallel)
Browse code

added function for resolving ambiguous protein names

Nils Kurzawa authored on 20/01/2020 09:31:59
Showing 1 changed files
NAMESPACE
History View file @ 89deb00
... ... 
@@ -25,6 +25,7 @@ export(plot2dTppProfile)
25 25 
 export(plot2dTppRelProfile)
26 26 
 export(recomputeSignalFromRatios)
27 27 
 export(renameColumns)
28 
+export(resolveAmbigousProteinNames)
28 29 
 export(runTPP2D)
29 30 
 exportClasses(tpp2dExperiment)
30 31 
 import(BiocParallel)
Browse code

deprecated computeFdr and replaced it by getFDR

Nils Kurzawa authored on 18/01/2020 19:33:55
Showing 1 changed files
NAMESPACE
History View file @ 7a03d6a
... ... 
@@ -15,6 +15,7 @@ export(findHits)
15 15 
 export(fitAndEvalDataset)
16 16 
 export(fitH0Model)
17 17 
 export(fitH1Model)
18 
+export(getFDR)
18 19 
 export(getModelParamsDf)
19 20 
 export(gg_qq)
20 21 
 export(import2dDataset)
Browse code

completed update to new bootstrap method based on alternative model residuals and adapted full workflow

Nils Kurzawa authored on 16/01/2020 16:11:08
Showing 1 changed files
NAMESPACE
History View file @ b3b3c63
... ... 
@@ -5,6 +5,7 @@ export(annotateDataList)
5 5 
 export(bootstrapNull)
6 6 
 export(bootstrapNullAlternativeModel)
7 7 
 export(competeModels)
8 
+export(computeFStatFromParams)
8 9 
 export(computeFdr)
9 10 
 export(computeFstat)
10 11 
 export(computePvalFromKernelDensity)
... ... 
@@ -34,6 +35,7 @@ importFrom(doParallel,registerDoParallel)
34 35 
 importFrom(foreach,"%dopar%")
35 36 
 importFrom(foreach,foreach)
36 37 
 importFrom(methods,is)
38 
+importFrom(methods,new)
37 39 
 importFrom(openxlsx,read.xlsx)
38 40 
 importFrom(parallel,makeCluster)
39 41 
 importFrom(parallel,stopCluster)
... ... 
@@ -52,5 +54,6 @@ importFrom(stats,sd)
52 54 
 importFrom(stringr,str_to_title)
53 55 
 importFrom(tidyr,gather)
54 56 
 importFrom(tidyr,spread)
57 
+importFrom(utils,head)
55 58 
 importFrom(utils,read.delim)
56 59 
 importFrom(utils,read.table)
Browse code

several changes to enable new workflow with bootstrapped null distribution based on alternative model residuals

Nils Kurzawa authored on 15/01/2020 17:33:34
Showing 1 changed files
NAMESPACE
History View file @ 3e7ff40
... ... 
@@ -23,7 +23,9 @@ export(plot2dTppProfile)
23 23 
 export(plot2dTppRelProfile)
24 24 
 export(recomputeSignalFromRatios)
25 25 
 export(renameColumns)
26 
+export(runTPP2D)
26 27 
 exportClasses(tpp2dExperiment)
28 
+import(BiocParallel)
27 29 
 import(dplyr)
28 30 
 import(ggplot2)
29 31 
 importFrom(MASS,lda)
Browse code

added function to globally estimate model parameters, added tpp2dExperiment class

Nils Kurzawa authored on 15/01/2020 12:34:07
Showing 1 changed files
NAMESPACE
History View file @ 9ecf848
... ... 
@@ -3,6 +3,7 @@
3 3 
 export(TPP_importCheckConfigTable)
4 4 
 export(annotateDataList)
5 5 
 export(bootstrapNull)
6 
+export(bootstrapNullAlternativeModel)
6 7 
 export(competeModels)
7 8 
 export(computeFdr)
8 9 
 export(computeFstat)
... ... 
@@ -13,6 +14,7 @@ export(findHits)
13 14 
 export(fitAndEvalDataset)
14 15 
 export(fitH0Model)
15 16 
 export(fitH1Model)
17 
+export(getModelParamsDf)
16 18 
 export(gg_qq)
17 19 
 export(import2dDataset)
18 20 
 export(import2dMain)
... ... 
@@ -21,6 +23,7 @@ export(plot2dTppProfile)
21 23 
 export(plot2dTppRelProfile)
22 24 
 export(recomputeSignalFromRatios)
23 25 
 export(renameColumns)
26 
+exportClasses(tpp2dExperiment)
24 27 
 import(dplyr)
25 28 
 import(ggplot2)
26 29 
 importFrom(MASS,lda)
Browse code

added alternative function for assessing FDR via kernel density derived p-values

Nils Kurzawa authored on 29/10/2019 16:15:10
Showing 1 changed files
NAMESPACE
History View file @ ccd57a2
... ... 
@@ -6,6 +6,7 @@ export(bootstrapNull)
6 6 
 export(competeModels)
7 7 
 export(computeFdr)
8 8 
 export(computeFstat)
9 
+export(computePvalFromKernelDensity)
9 10 
 export(configWide2Long)
10 11 
 export(filterOutContaminants)
11 12 
 export(findHits)
... ... 
@@ -31,12 +32,15 @@ importFrom(methods,is)
31 32 
 importFrom(openxlsx,read.xlsx)
32 33 
 importFrom(parallel,makeCluster)
33 34 
 importFrom(parallel,stopCluster)
35 
+importFrom(sfsmisc,integrate.xy)
34 36 
 importFrom(stats,approx)
35 37 
 importFrom(stats,coef)
38 
+importFrom(stats,density)
36 39 
 importFrom(stats,fft)
37 40 
 importFrom(stats,lm)
38 41 
 importFrom(stats,median)
39 42 
 importFrom(stats,optim)
43 
+importFrom(stats,p.adjust)
40 44 
 importFrom(stats,predict)
41 45 
 importFrom(stats,residuals)
42 46 
 importFrom(stats,sd)
Browse code

removed moderate outlier function, since outlier moderation was evaluated to compromise FDR control

Nils Kurzawa authored on 16/08/2019 10:06:40
Showing 1 changed files
NAMESPACE
History View file @ c1e8b49
... ... 
@@ -15,7 +15,6 @@ export(fitH1Model)
15 15 
 export(gg_qq)
16 16 
 export(import2dDataset)
17 17 
 export(import2dMain)
18 
-export(moderateOutliers)
19 18 
 export(plot2dTppFit)
20 19 
 export(plot2dTppProfile)
21 20 
 export(plot2dTppRelProfile)
Browse code

added function for outlier moderation, adapted test for new boostrapping method

Nils Kurzawa authored on 17/06/2019 16:46:34
Showing 1 changed files
NAMESPACE
History View file @ 4e5b29b
... ... 
@@ -15,6 +15,7 @@ export(fitH1Model)
15 15 
 export(gg_qq)
16 16 
 export(import2dDataset)
17 17 
 export(import2dMain)
18 
+export(moderateOutliers)
18 19 
 export(plot2dTppFit)
19 20 
 export(plot2dTppProfile)
20 21 
 export(plot2dTppRelProfile)
... ... 
@@ -39,6 +40,7 @@ importFrom(stats,median)
39 40 
 importFrom(stats,optim)
40 41 
 importFrom(stats,predict)
41 42 
 importFrom(stats,residuals)
43 
+importFrom(stats,sd)
42 44 
 importFrom(stringr,str_to_title)
43 45 
 importFrom(tidyr,gather)
44 46 
 importFrom(tidyr,spread)
Browse code

modified DESCRIPTION to contain co-authors, carry-over detection now works with a lda model, updated NEWS file

Nils Kurzawa authored on 07/05/2019 08:21:46
Showing 1 changed files
NAMESPACE
History View file @ f9d7a21
... ... 
@@ -22,6 +22,7 @@ export(recomputeSignalFromRatios)
22 22 
 export(renameColumns)
23 23 
 import(dplyr)
24 24 
 import(ggplot2)
25 
+importFrom(MASS,lda)
25 26 
 importFrom(RCurl,url.exists)
26 27 
 importFrom(doParallel,registerDoParallel)
27 28 
 importFrom(foreach,"%dopar%")
Browse code

changed dataset documentation accorsing to BioC review suggestions, included possbility to resample residuals within MS experiments during null bootstrapping

Nils Kurzawa authored on 23/04/2019 07:31:37
Showing 1 changed files
NAMESPACE
History View file @ 94916b8
... ... 
@@ -36,6 +36,7 @@ importFrom(stats,fft)
36 36 
 importFrom(stats,lm)
37 37 
 importFrom(stats,median)
38 38 
 importFrom(stats,optim)
39 
+importFrom(stats,predict)
39 40 
 importFrom(stats,residuals)
40 41 
 importFrom(stringr,str_to_title)
41 42 
 importFrom(tidyr,gather)
Browse code

adressed review comments as well as possibe

Nils Kurzawa authored on 15/04/2019 08:31:14
Showing 1 changed files
NAMESPACE
History View file @ 02d6d7b
... ... 
@@ -1,19 +1,25 @@
1 1 
 # Generated by roxygen2: do not edit by hand
2 2
3 
+export(TPP_importCheckConfigTable)
4 
+export(annotateDataList)
3 5 
 export(bootstrapNull)
4 6 
 export(competeModels)
5 7 
 export(computeFdr)
6 8 
 export(computeFstat)
9 
+export(configWide2Long)
10 
+export(filterOutContaminants)
7 11 
 export(findHits)
8 12 
 export(fitAndEvalDataset)
9 13 
 export(fitH0Model)
10 14 
 export(fitH1Model)
11 15 
 export(gg_qq)
12 16 
 export(import2dDataset)
17 
+export(import2dMain)
13 18 
 export(plot2dTppFit)
14 19 
 export(plot2dTppProfile)
15 20 
 export(plot2dTppRelProfile)
16 21 
 export(recomputeSignalFromRatios)
22 
+export(renameColumns)
17 23 
 import(dplyr)
18 24 
 import(ggplot2)
19 25 
 importFrom(RCurl,url.exists)
... ... 
@@ -26,6 +32,7 @@ importFrom(parallel,makeCluster)
26 32 
 importFrom(parallel,stopCluster)
27 33 
 importFrom(stats,approx)
28 34 
 importFrom(stats,coef)
35 
+importFrom(stats,fft)
29 36 
 importFrom(stats,lm)
30 37 
 importFrom(stats,median)
31 38 
 importFrom(stats,optim)
Browse code

changed doParallel call in bootstrapNull function to hopefully run on windows re-added examples for functions using bootstrapNull function in example, bumped version to 0.99.6

Nils Kurzawa authored on 14/03/2019 10:01:57
Showing 1 changed files
NAMESPACE
History View file @ 0d47223
... ... 
@@ -22,6 +22,8 @@ importFrom(foreach,"%dopar%")
22 22 
 importFrom(foreach,foreach)
23 23 
 importFrom(methods,is)
24 24 
 importFrom(openxlsx,read.xlsx)
25 
+importFrom(parallel,makeCluster)
26 
+importFrom(parallel,stopCluster)
25 27 
 importFrom(stats,approx)
26 28 
 importFrom(stats,coef)
27 29 
 importFrom(stats,lm)
Browse code

resolved more visible binding problems replaced example data once more to include correct concentrations for tru positives

Nils Kurzawa authored on 04/02/2019 18:09:22
Showing 1 changed files
NAMESPACE
History View file @ d96a18d
... ... 
@@ -16,9 +16,11 @@ export(plot2dTppRelProfile)
16 16 
 export(recomputeSignalFromRatios)
17 17 
 import(dplyr)
18 18 
 import(ggplot2)
19 
+importFrom(RCurl,url.exists)
19 20 
 importFrom(doParallel,registerDoParallel)
20 21 
 importFrom(foreach,"%dopar%")
21 22 
 importFrom(foreach,foreach)
23 
+importFrom(methods,is)
22 24 
 importFrom(openxlsx,read.xlsx)
23 25 
 importFrom(stats,approx)
24 26 
 importFrom(stats,coef)
Browse code

started fixing biocCheck errors

Nils Kurzawa authored on 30/01/2019 17:04:20
Showing 1 changed files
NAMESPACE
History View file @ fa7d9b0
... ... 
@@ -21,9 +21,13 @@ importFrom(foreach,"%dopar%")
21 21 
 importFrom(foreach,foreach)
22 22 
 importFrom(openxlsx,read.xlsx)
23 23 
 importFrom(stats,approx)
24 
+importFrom(stats,coef)
24 25 
 importFrom(stats,lm)
26 
+importFrom(stats,median)
25 27 
 importFrom(stats,optim)
28 
+importFrom(stats,residuals)
26 29 
 importFrom(stringr,str_to_title)
27 30 
 importFrom(tidyr,gather)
31 
+importFrom(tidyr,spread)
28 32 
 importFrom(utils,read.delim)
29 33 
 importFrom(utils,read.table)
Browse code

removed TPP package dependency

Nils Kurzawa authored on 25/01/2019 16:33:43
Showing 1 changed files
NAMESPACE
History View file @ 342fc17
... ... 
@@ -10,16 +10,20 @@ export(fitH0Model)
10 10 
 export(fitH1Model)
11 11 
 export(gg_qq)
12 12 
 export(import2dDataset)
13 
-export(nullSampleFstat)
14 13 
 export(plot2dTppFit)
15 14 
 export(plot2dTppProfile)
16 15 
 export(plot2dTppRelProfile)
17 16 
 export(recomputeSignalFromRatios)
18 
-import(TPP)
19 17 
 import(dplyr)
20 18 
 import(ggplot2)
21 19 
 importFrom(doParallel,registerDoParallel)
22 20 
 importFrom(foreach,"%dopar%")
23 21 
 importFrom(foreach,foreach)
22 
+importFrom(openxlsx,read.xlsx)
24 23 
 importFrom(stats,approx)
25 24 
 importFrom(stats,lm)
25 
+importFrom(stats,optim)
26 
+importFrom(stringr,str_to_title)
27 
+importFrom(tidyr,gather)
28 
+importFrom(utils,read.delim)
29 
+importFrom(utils,read.table)
Browse code

warped up package so far that running full workflow is possible

Nils Kurzawa authored on 23/01/2019 17:39:32
Showing 1 changed files
NAMESPACE
History View file @ bf1405f
... ... 
@@ -1,6 +1,7 @@
1 1 
 # Generated by roxygen2: do not edit by hand
2 2
3 3 
 export(bootstrapNull)
4 
+export(competeModels)
4 5 
 export(computeFdr)
5 6 
 export(computeFstat)
6 7 
 export(findHits)
... ... 
@@ -9,6 +10,8 @@ export(fitH0Model)
9 10 
 export(fitH1Model)
10 11 
 export(gg_qq)
11 12 
 export(import2dDataset)
13 
+export(nullSampleFstat)
14 
+export(plot2dTppFit)
12 15 
 export(plot2dTppProfile)
13 16 
 export(plot2dTppRelProfile)
14 17 
 export(recomputeSignalFromRatios)
Browse code

created wrapper functions for model fitting and bootstrapping, added TPP as bioC package to travis file

Nils Kurzawa authored on 16/01/2019 17:34:25
Showing 1 changed files
NAMESPACE
History View file @ 29b04a6
... ... 
@@ -1,11 +1,22 @@
1 1 
 # Generated by roxygen2: do not edit by hand
2 2
3 
+export(bootstrapNull)
4 
+export(computeFdr)
5 
+export(computeFstat)
6 
+export(findHits)
7 
+export(fitAndEvalDataset)
3 8 
 export(fitH0Model)
4 9 
 export(fitH1Model)
5 10 
 export(gg_qq)
11 
+export(import2dDataset)
6 12 
 export(plot2dTppProfile)
7 13 
 export(plot2dTppRelProfile)
8 14 
 export(recomputeSignalFromRatios)
15 
+import(TPP)
9 16 
 import(dplyr)
10 17 
 import(ggplot2)
18 
+importFrom(doParallel,registerDoParallel)
19 
+importFrom(foreach,"%dopar%")
20 
+importFrom(foreach,foreach)
11 21 
 importFrom(stats,approx)
22 
+importFrom(stats,lm)
Browse code

added missing parameter descriptions for model fit functions

Nils Kurzawa authored on 14/01/2019 17:36:14
Showing 1 changed files
NAMESPACE
History View file @ 4e5ade5
... ... 
@@ -9,6 +9,3 @@ export(recomputeSignalFromRatios)
9 9 
 import(dplyr)
10 10 
 import(ggplot2)
11 11 
 importFrom(stats,approx)
12 
-useDynLib(TPP2D, .registration=TRUE)
13 
-exportPattern("^[[:alpha:]]+")
14 
-importFrom(Rcpp, evalCpp)
Browse code

added cpp implementation for optimization and gradient function

Nils Kurzawa authored on 14/01/2019 17:25:14
Showing 1 changed files
NAMESPACE
History View file @ d05512c
... ... 
@@ -1,5 +1,7 @@
1 1 
 # Generated by roxygen2: do not edit by hand
2 2
3 
+export(fitH0Model)
4 
+export(fitH1Model)
3 5 
 export(gg_qq)
4 6 
 export(plot2dTppProfile)
5 7 
 export(plot2dTppRelProfile)
... ... 
@@ -7,3 +9,6 @@ export(recomputeSignalFromRatios)
7 9 
 import(dplyr)
8 10 
 import(ggplot2)
9 11 
 importFrom(stats,approx)
12 
+useDynLib(TPP2D, .registration=TRUE)
13 
+exportPattern("^[[:alpha:]]+")
14 
+importFrom(Rcpp, evalCpp)
Browse code

added first plot functions and changed DESCRIPTION file dependency to a 'zero'-level R version

Nils Kurzawa authored on 22/12/2018 11:42:30
Showing 1 changed files
NAMESPACE
History View file @ 50fb6a6
... ... 
@@ -1,4 +1,9 @@
1 1 
 # Generated by roxygen2: do not edit by hand
2 2
3 
+export(gg_qq)
4 
+export(plot2dTppProfile)
5 
+export(plot2dTppRelProfile)
3 6 
 export(recomputeSignalFromRatios)
4 7 
 import(dplyr)
8 
+import(ggplot2)
9 
+importFrom(stats,approx)
Browse code

initial package setup and recompute signal from ratios functions including test

Nils Kurzawa authored on 18/12/2018 15:43:29
Showing 1 changed files
NAMESPACE
History View file @ 494b90f
1 1 
new file mode 100644
... ... 
@@ -0,0 +1,4 @@
1 
+# Generated by roxygen2: do not edit by hand
2 
+
3 
+export(recomputeSignalFromRatios)
4 
+import(dplyr)