diff --git a/DESCRIPTION b/DESCRIPTION
index cdc2e2f..e685a4b 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -2,7 +2,7 @@ Package: SRMService
Type: Package
Title: Report Quantitative Mass Spectrometry Data
Date: 2018-09-10
-Version: 0.1.9.23
+Version: 0.1.9.24
Authors@R: c(person("Witold", "Wolski", email = "wewolski@gmail.com", role = c("aut", "cre")),
person("Jonas", "Grossmann", email = "jg@fgcz.ethz.ch", role = c("aut")),
person("Christian", "Panse", email = "cp@fgcz.ethz.ch", role = c("aut")))
@@ -38,14 +38,23 @@ Imports:
usethis,
yaml
Suggests:
- missForest
+ missForest,
+ testthat,
+ ggplot2,
+ knitr,
+ readxl,
+ MSqRob
+Remotes:
+ protViz/quantable,
+ statOmics/MSqRob
License: GPL
LazyData: TRUE
URL: https://github.com/protViz/SRMService
BugReports: https://github.com/protViz/SRMService/issues
Repository: CRAN
-RoxygenNote: 6.1.1
-Collate:
+RoxygenNote: 7.1.1
+VignetteBuilder: knitr
+Collate:
'A_dataset_docu.R'
'RequiredColumns.R'
'eb.fit.R'
@@ -64,14 +73,5 @@ Collate:
'readMaxQuant.R'
'transitionCorrelations.R'
'zzz.R'
-Suggests:
- testthat,
- ggplot2,
- knitr,
- readxl,
- MSqRob
-Remotes:
- protViz/quantable,
- protViz/bibliospec,
- statOmics/MSqRob
-VignetteBuilder: knitr
+Depends:
+ R (>= 2.10)
diff --git a/R/PrepareRmdAnalysisEnv.R b/R/PrepareRmdAnalysisEnv.R
index 186b2b1..b74c8c4 100644
--- a/R/PrepareRmdAnalysisEnv.R
+++ b/R/PrepareRmdAnalysisEnv.R
@@ -36,8 +36,8 @@ RMD_MQ_Quant_2GrpAnalysis <- function(workdir = getwd()){
.scriptCopyHelperVec(c("/RunScripts/Run_MQ_QuantTwoGroupAnalysis.R",
"/doc/Grp2Analysis.Rmd",
"/doc/bibliography.bib",
- "/doc/Grp2Analysis_Empty.Rmd_t",
- "/doc/Grp2Analysis_MissingInOneCondition.Rmd_t"), workdir = workdir )
+ "/doc/Grp2Analysis_MissingInOneCondition.Rmd",
+ "/doc/Empty.Rmd"), workdir = workdir )
}
#' copies the RMD and Run files for 2 grp analysis based on a PD (protein discoverer) in your working directory.
diff --git a/man/Annotation.Rd b/man/Annotation.Rd
index dff8163..f4e1c14 100644
--- a/man/Annotation.Rd
+++ b/man/Annotation.Rd
@@ -4,11 +4,9 @@
\name{Annotation}
\alias{Annotation}
\title{Condition Map}
-\format{An object of class \code{R6ClassGenerator} of length 24.}
-\usage{
-Annotation
-}
\description{
+Condition Map
+
Condition Map
}
\examples{
@@ -29,4 +27,117 @@ cm$sampleID
cm$get_sample_id()
cm$annotation
}
-\keyword{datasets}
+\section{Methods}{
+\subsection{Public methods}{
+\itemize{
+\item \href{#method-new}{\code{Annotation$new()}}
+\item \href{#method-exists}{\code{Annotation$exists()}}
+\item \href{#method-levels}{\code{Annotation$levels()}}
+\item \href{#method-get}{\code{Annotation$get()}}
+\item \href{#method-get_factors}{\code{Annotation$get_factors()}}
+\item \href{#method-get_sample_id}{\code{Annotation$get_sample_id()}}
+\item \href{#method-as_numeric}{\code{Annotation$as_numeric()}}
+\item \href{#method-get_color}{\code{Annotation$get_color()}}
+\item \href{#method-clone}{\code{Annotation$clone()}}
+}
+}
+\if{html}{\out{
}}
+\if{html}{\out{}}
+\if{latex}{\out{\hypertarget{method-new}{}}}
+\subsection{Method \code{new()}}{
+\subsection{Usage}{
+\if{html}{\out{}}\preformatted{Annotation$new(
+ annotation,
+ experimentID,
+ fixed = NULL,
+ random = NULL,
+ sampleID = "Raw.file"
+)}\if{html}{\out{
}}
+}
+
+}
+\if{html}{\out{
}}
+\if{html}{\out{}}
+\if{latex}{\out{\hypertarget{method-exists}{}}}
+\subsection{Method \code{exists()}}{
+\subsection{Usage}{
+\if{html}{\out{}}\preformatted{Annotation$exists(colname)}\if{html}{\out{
}}
+}
+
+}
+\if{html}{\out{
}}
+\if{html}{\out{}}
+\if{latex}{\out{\hypertarget{method-levels}{}}}
+\subsection{Method \code{levels()}}{
+\subsection{Usage}{
+\if{html}{\out{}}\preformatted{Annotation$levels(colname)}\if{html}{\out{
}}
+}
+
+}
+\if{html}{\out{
}}
+\if{html}{\out{}}
+\if{latex}{\out{\hypertarget{method-get}{}}}
+\subsection{Method \code{get()}}{
+\subsection{Usage}{
+\if{html}{\out{}}\preformatted{Annotation$get(colname)}\if{html}{\out{
}}
+}
+
+}
+\if{html}{\out{
}}
+\if{html}{\out{}}
+\if{latex}{\out{\hypertarget{method-get_factors}{}}}
+\subsection{Method \code{get_factors()}}{
+\subsection{Usage}{
+\if{html}{\out{}}\preformatted{Annotation$get_factors()}\if{html}{\out{
}}
+}
+
+}
+\if{html}{\out{
}}
+\if{html}{\out{}}
+\if{latex}{\out{\hypertarget{method-get_sample_id}{}}}
+\subsection{Method \code{get_sample_id()}}{
+\subsection{Usage}{
+\if{html}{\out{}}\preformatted{Annotation$get_sample_id()}\if{html}{\out{
}}
+}
+
+}
+\if{html}{\out{
}}
+\if{html}{\out{}}
+\if{latex}{\out{\hypertarget{method-as_numeric}{}}}
+\subsection{Method \code{as_numeric()}}{
+\subsection{Usage}{
+\if{html}{\out{}}\preformatted{Annotation$as_numeric(colname)}\if{html}{\out{
}}
+}
+
+}
+\if{html}{\out{
}}
+\if{html}{\out{}}
+\if{latex}{\out{\hypertarget{method-get_color}{}}}
+\subsection{Method \code{get_color()}}{
+\subsection{Usage}{
+\if{html}{\out{}}\preformatted{Annotation$get_color(
+ colname,
+ pal_function = dichromat_pal,
+ pal_name = "BrowntoBlue.10"
+)}\if{html}{\out{
}}
+}
+
+}
+\if{html}{\out{
}}
+\if{html}{\out{}}
+\if{latex}{\out{\hypertarget{method-clone}{}}}
+\subsection{Method \code{clone()}}{
+The objects of this class are cloneable with this method.
+\subsection{Usage}{
+\if{html}{\out{}}\preformatted{Annotation$clone(deep = FALSE)}\if{html}{\out{
}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{}}
+\describe{
+\item{\code{deep}}{Whether to make a deep clone.}
+}
+\if{html}{\out{
}}
+}
+}
+}
diff --git a/man/Grp2Analysis-class.Rd b/man/Grp2Analysis-class.Rd
index 3dd89a0..c40f879 100644
--- a/man/Grp2Analysis-class.Rd
+++ b/man/Grp2Analysis-class.Rd
@@ -59,8 +59,7 @@ Perform 2 group analysis with visualization
\item{\code{setMQProteinGroups(MQProteinGroups)}}{set MQ protein groups table}
-\item{\code{setNormalizationMethod(normalizationMethod = "robustscale",
- housekeeper = "")}}{set the normalization parameters}
+\item{\code{setNormalizationMethod(normalizationMethod = "robustscale", housekeeper = "")}}{set the normalization parameters}
\item{\code{setProteins(protein)}}{used to verify proteingroups structure and set members}
}}
diff --git a/man/MQtoMSstatsFormat.Rd b/man/MQtoMSstatsFormat.Rd
index d37cde4..9f4ce2e 100644
--- a/man/MQtoMSstatsFormat.Rd
+++ b/man/MQtoMSstatsFormat.Rd
@@ -4,9 +4,15 @@
\alias{MQtoMSstatsFormat}
\title{MaxQtoMSstatsFormat}
\usage{
-MQtoMSstatsFormat(evidence, annotation, proteinGroups,
- useUniquePeptide = TRUE, summaryforMultipleRows = max,
- fewMeasurements = "remove", removeMpeptides = TRUE)
+MQtoMSstatsFormat(
+ evidence,
+ annotation,
+ proteinGroups,
+ useUniquePeptide = TRUE,
+ summaryforMultipleRows = max,
+ fewMeasurements = "remove",
+ removeMpeptides = TRUE
+)
}
\arguments{
\item{evidence}{MQ evidence.txt read using read.csv(sep=\"\\t\")}
diff --git a/man/ProteinTableR6.Rd b/man/ProteinTableR6.Rd
index a22670a..64d4853 100644
--- a/man/ProteinTableR6.Rd
+++ b/man/ProteinTableR6.Rd
@@ -4,21 +4,11 @@
\name{ProteinTableR6}
\alias{ProteinTableR6}
\title{Protein Table}
-\format{An object of class \code{R6ClassGenerator} of length 24.}
-\usage{
-ProteinTableR6
-}
\description{
Protein Table
-}
-\section{Fields}{
-
-\describe{
-\item{\code{data}}{data.frame with colnames sample ID rownames proteinID}
-
-\item{\code{experimentID}}{name of the experiment}
-}}
+Protein Table
+}
\examples{
library(SRMService)
x <- data.frame(Raw.file = c("A","B","C"),"MeasurementOrder" = c(1,2,3) , Gender = c("F","F","M"))
@@ -32,4 +22,117 @@ pt$get_data_long()
pt$get_data_wide()
pt$get_all_long()
}
-\keyword{datasets}
+\section{Public fields}{
+\if{html}{\out{}}
+\describe{
+\item{\code{data}}{data.frame with colnames sample ID rownames proteinID}
+
+\item{\code{experimentID}}{name of the experiment}
+}
+\if{html}{\out{
}}
+}
+\section{Active bindings}{
+\if{html}{\out{}}
+\describe{
+\item{\code{experimentID}}{name of the experiment}
+}
+\if{html}{\out{
}}
+}
+\section{Methods}{
+\subsection{Public methods}{
+\itemize{
+\item \href{#method-new}{\code{ProteinTableR6$new()}}
+\item \href{#method-set_data_wide}{\code{ProteinTableR6$set_data_wide()}}
+\item \href{#method-get_protein_id}{\code{ProteinTableR6$get_protein_id()}}
+\item \href{#method-get_data_long}{\code{ProteinTableR6$get_data_long()}}
+\item \href{#method-get_all_long}{\code{ProteinTableR6$get_all_long()}}
+\item \href{#method-get_data_wide}{\code{ProteinTableR6$get_data_wide()}}
+\item \href{#method-get_annotation}{\code{ProteinTableR6$get_annotation()}}
+\item \href{#method-clone}{\code{ProteinTableR6$clone()}}
+}
+}
+\if{html}{\out{
}}
+\if{html}{\out{}}
+\if{latex}{\out{\hypertarget{method-new}{}}}
+\subsection{Method \code{new()}}{
+\subsection{Usage}{
+\if{html}{\out{}}\preformatted{ProteinTableR6$new(
+ annotation,
+ proteinID = "proteinID",
+ required = c("NrPeptides", "Fasta.Headers")
+)}\if{html}{\out{
}}
+}
+
+}
+\if{html}{\out{
}}
+\if{html}{\out{}}
+\if{latex}{\out{\hypertarget{method-set_data_wide}{}}}
+\subsection{Method \code{set_data_wide()}}{
+\subsection{Usage}{
+\if{html}{\out{}}\preformatted{ProteinTableR6$set_data_wide(data)}\if{html}{\out{
}}
+}
+
+}
+\if{html}{\out{
}}
+\if{html}{\out{}}
+\if{latex}{\out{\hypertarget{method-get_protein_id}{}}}
+\subsection{Method \code{get_protein_id()}}{
+\subsection{Usage}{
+\if{html}{\out{}}\preformatted{ProteinTableR6$get_protein_id()}\if{html}{\out{
}}
+}
+
+}
+\if{html}{\out{
}}
+\if{html}{\out{}}
+\if{latex}{\out{\hypertarget{method-get_data_long}{}}}
+\subsection{Method \code{get_data_long()}}{
+\subsection{Usage}{
+\if{html}{\out{}}\preformatted{ProteinTableR6$get_data_long()}\if{html}{\out{
}}
+}
+
+}
+\if{html}{\out{
}}
+\if{html}{\out{}}
+\if{latex}{\out{\hypertarget{method-get_all_long}{}}}
+\subsection{Method \code{get_all_long()}}{
+\subsection{Usage}{
+\if{html}{\out{}}\preformatted{ProteinTableR6$get_all_long()}\if{html}{\out{
}}
+}
+
+}
+\if{html}{\out{
}}
+\if{html}{\out{}}
+\if{latex}{\out{\hypertarget{method-get_data_wide}{}}}
+\subsection{Method \code{get_data_wide()}}{
+\subsection{Usage}{
+\if{html}{\out{}}\preformatted{ProteinTableR6$get_data_wide()}\if{html}{\out{
}}
+}
+
+}
+\if{html}{\out{
}}
+\if{html}{\out{}}
+\if{latex}{\out{\hypertarget{method-get_annotation}{}}}
+\subsection{Method \code{get_annotation()}}{
+\subsection{Usage}{
+\if{html}{\out{}}\preformatted{ProteinTableR6$get_annotation()}\if{html}{\out{
}}
+}
+
+}
+\if{html}{\out{
}}
+\if{html}{\out{}}
+\if{latex}{\out{\hypertarget{method-clone}{}}}
+\subsection{Method \code{clone()}}{
+The objects of this class are cloneable with this method.
+\subsection{Usage}{
+\if{html}{\out{}}\preformatted{ProteinTableR6$clone(deep = FALSE)}\if{html}{\out{
}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{}}
+\describe{
+\item{\code{deep}}{Whether to make a deep clone.}
+}
+\if{html}{\out{
}}
+}
+}
+}
diff --git a/man/ProteinVariableSelect.Rd b/man/ProteinVariableSelect.Rd
index 1ea35f4..52befa7 100644
--- a/man/ProteinVariableSelect.Rd
+++ b/man/ProteinVariableSelect.Rd
@@ -1,14 +1,84 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/R6_ProteinVariableSelect.R
-\docType{data}
\name{ProteinVariableSelect}
\alias{ProteinVariableSelect}
\title{Wraps 4 column matrix, with Condition, Run, Protein, Intensity}
-\format{An object of class \code{R6ClassGenerator} of length 24.}
-\usage{
-ProteinVariableSelect
-}
\description{
Wraps 4 column matrix, with Condition, Run, Protein, Intensity
+
+Wraps 4 column matrix, with Condition, Run, Protein, Intensity
+}
+\section{Methods}{
+\subsection{Public methods}{
+\itemize{
+\item \href{#method-new}{\code{ProteinVariableSelect$new()}}
+\item \href{#method-getIntensities}{\code{ProteinVariableSelect$getIntensities()}}
+\item \href{#method-getWideFormat}{\code{ProteinVariableSelect$getWideFormat()}}
+\item \href{#method-getWideNoMissing}{\code{ProteinVariableSelect$getWideNoMissing()}}
+\item \href{#method-getIntensitiesNoMissing}{\code{ProteinVariableSelect$getIntensitiesNoMissing()}}
+\item \href{#method-clone}{\code{ProteinVariableSelect$clone()}}
+}
+}
+\if{html}{\out{
}}
+\if{html}{\out{}}
+\if{latex}{\out{\hypertarget{method-new}{}}}
+\subsection{Method \code{new()}}{
+\subsection{Usage}{
+\if{html}{\out{}}\preformatted{ProteinVariableSelect$new(data)}\if{html}{\out{
}}
+}
+
+}
+\if{html}{\out{
}}
+\if{html}{\out{}}
+\if{latex}{\out{\hypertarget{method-getIntensities}{}}}
+\subsection{Method \code{getIntensities()}}{
+\subsection{Usage}{
+\if{html}{\out{}}\preformatted{ProteinVariableSelect$getIntensities()}\if{html}{\out{
}}
+}
+
+}
+\if{html}{\out{
}}
+\if{html}{\out{}}
+\if{latex}{\out{\hypertarget{method-getWideFormat}{}}}
+\subsection{Method \code{getWideFormat()}}{
+\subsection{Usage}{
+\if{html}{\out{}}\preformatted{ProteinVariableSelect$getWideFormat()}\if{html}{\out{
}}
+}
+
+}
+\if{html}{\out{
}}
+\if{html}{\out{}}
+\if{latex}{\out{\hypertarget{method-getWideNoMissing}{}}}
+\subsection{Method \code{getWideNoMissing()}}{
+\subsection{Usage}{
+\if{html}{\out{}}\preformatted{ProteinVariableSelect$getWideNoMissing()}\if{html}{\out{
}}
+}
+
+}
+\if{html}{\out{
}}
+\if{html}{\out{}}
+\if{latex}{\out{\hypertarget{method-getIntensitiesNoMissing}{}}}
+\subsection{Method \code{getIntensitiesNoMissing()}}{
+\subsection{Usage}{
+\if{html}{\out{}}\preformatted{ProteinVariableSelect$getIntensitiesNoMissing()}\if{html}{\out{
}}
+}
+
+}
+\if{html}{\out{
}}
+\if{html}{\out{}}
+\if{latex}{\out{\hypertarget{method-clone}{}}}
+\subsection{Method \code{clone()}}{
+The objects of this class are cloneable with this method.
+\subsection{Usage}{
+\if{html}{\out{}}\preformatted{ProteinVariableSelect$clone(deep = FALSE)}\if{html}{\out{
}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{}}
+\describe{
+\item{\code{deep}}{Whether to make a deep clone.}
+}
+\if{html}{\out{
}}
+}
+}
}
-\keyword{datasets}
diff --git a/man/annotationColumns.Rd b/man/annotationColumns.Rd
index 9a374bc..68f7e27 100644
--- a/man/annotationColumns.Rd
+++ b/man/annotationColumns.Rd
@@ -4,7 +4,9 @@
\name{annotationColumns}
\alias{annotationColumns}
\title{Annotation Columns}
-\format{An object of class \code{character} of length 5.}
+\format{
+An object of class \code{character} of length 5.
+}
\usage{
annotationColumns
}
diff --git a/man/correlatedPeptideList.Rd b/man/correlatedPeptideList.Rd
index e9def26..5bb655c 100644
--- a/man/correlatedPeptideList.Rd
+++ b/man/correlatedPeptideList.Rd
@@ -4,7 +4,9 @@
\name{correlatedPeptideList}
\alias{correlatedPeptideList}
\title{List with peptide intensities}
-\format{A list of data frames}
+\format{
+A list of data frames
+}
\usage{
correlatedPeptideList
}
diff --git a/man/fgcz_render_One2OneReport.Rd b/man/fgcz_render_One2OneReport.Rd
index 87652ab..d5c6798 100644
--- a/man/fgcz_render_One2OneReport.Rd
+++ b/man/fgcz_render_One2OneReport.Rd
@@ -4,8 +4,10 @@
\alias{fgcz_render_One2OneReport}
\title{perform rendering}
\usage{
-fgcz_render_One2OneReport(maxquanttxtdirectory = ".",
- reportFileBaseName = "fgcz_MQ_QC_report")
+fgcz_render_One2OneReport(
+ maxquanttxtdirectory = ".",
+ reportFileBaseName = "fgcz_MQ_QC_report"
+)
}
\description{
perform rendering
diff --git a/man/genericQuantMatrixGRP2.Rd b/man/genericQuantMatrixGRP2.Rd
index 89870c6..92164a9 100644
--- a/man/genericQuantMatrixGRP2.Rd
+++ b/man/genericQuantMatrixGRP2.Rd
@@ -4,7 +4,9 @@
\name{genericQuantMatrixGRP2}
\alias{genericQuantMatrixGRP2}
\title{Grp2Analysis reference class for running 2 grp analysis}
-\format{reference class}
+\format{
+reference class
+}
\usage{
genericQuantMatrixGRP2
}
diff --git a/man/grp2PullDownExample.Rd b/man/grp2PullDownExample.Rd
index a6b2530..aea1182 100644
--- a/man/grp2PullDownExample.Rd
+++ b/man/grp2PullDownExample.Rd
@@ -4,7 +4,9 @@
\name{grp2PullDownExample}
\alias{grp2PullDownExample}
\title{Grp2Analysis on pulldown data example}
-\format{reference class}
+\format{
+reference class
+}
\usage{
grp2PullDownExample
}
diff --git a/man/mqQuantMatrixGRP2.Rd b/man/mqQuantMatrixGRP2.Rd
index 297460f..8c897ff 100644
--- a/man/mqQuantMatrixGRP2.Rd
+++ b/man/mqQuantMatrixGRP2.Rd
@@ -4,7 +4,9 @@
\name{mqQuantMatrixGRP2}
\alias{mqQuantMatrixGRP2}
\title{Grp2Analysis on of nockout with missing data}
-\format{reference class}
+\format{
+reference class
+}
\usage{
mqQuantMatrixGRP2
}
diff --git a/man/proteinColumns.Rd b/man/proteinColumns.Rd
index e45c5f9..c6d8feb 100644
--- a/man/proteinColumns.Rd
+++ b/man/proteinColumns.Rd
@@ -4,7 +4,9 @@
\name{proteinColumns}
\alias{proteinColumns}
\title{Protein Columns}
-\format{An object of class \code{character} of length 4.}
+\format{
+An object of class \code{character} of length 4.
+}
\usage{
proteinColumns
}
diff --git a/man/transitionCorrelationsJack.Rd b/man/transitionCorrelationsJack.Rd
index 80ccc0d..8534817 100644
--- a/man/transitionCorrelationsJack.Rd
+++ b/man/transitionCorrelationsJack.Rd
@@ -4,8 +4,11 @@
\alias{transitionCorrelationsJack}
\title{Compute correlation matrix with jack}
\usage{
-transitionCorrelationsJack(dataX, distmethod = function(x) { cor(x,
- use = "pairwise.complete.obs", method = "pearson") })
+transitionCorrelationsJack(
+ dataX,
+ distmethod = function(x) { cor(x, use = "pairwise.complete.obs", method =
+ "pearson") }
+)
}
\arguments{
\item{dataX}{data.frame with transition intensities per peptide}
diff --git a/vignettes/.install_extras b/vignettes/.install_extras
index a9fd4ad..380ee2a 100644
--- a/vignettes/.install_extras
+++ b/vignettes/.install_extras
@@ -1,2 +1,3 @@
bibliography.bib$
-Rmd_t$
+Grp2Analysis_MissingInOneCondition.Rmd$
+Empty.Rmd$
diff --git a/vignettes/Grp2Analysis.Rmd b/vignettes/Grp2Analysis.Rmd
index ae60134..61debf7 100644
--- a/vignettes/Grp2Analysis.Rmd
+++ b/vignettes/Grp2Analysis.Rmd
@@ -57,7 +57,7 @@ library(rlang)
The following analysis compares protein signal intensities recorded in two groups of samples (Tables \@ref(tab:samples) and \@ref(tab:annotation)) by computing the fold change $log2(condition/reference)$ (difference between the means in both groups - also called effect size), and testing if it is different from zero. Table \@ref(tab:groupingvars) shows the group used as the reference.
-The protein identification and quantification were performed using the _MaxQuant_ software and _Andromeda_ search engine [@Cox2008, @Cox2011]. Based on the `proteinGroups.txt` file we generated by MaxQuant; we run a set of functions implemented in the R package SRMService [@SRMService2018] to generate visualizations and to compute
+The protein identification and quantification were performed using the _MaxQuant_ software and _Andromeda_ search engine [@Cox2008; @Cox2011]. Based on the `proteinGroups.txt` file we generated by MaxQuant; we run a set of functions implemented in the R package SRMService [@SRMService2018] to generate visualizations and to compute
a _moderated t-test_ [@Smyth2004] for all proteins quantified with at least `r grp2$nrPeptides` peptides, employing the R package limma [@Ritchie2015a].
@@ -373,19 +373,21 @@ ggplot(top20CI, aes(x = proteinID, y = log2FC,
results <- grp2$getResultTable()
NAinfo <- c(sum(is.na(results[, grp2$getConditions()$reference])) ,
sum(is.na(results[, grp2$getConditions()$condition])) )
-NAinfo<-data.frame(name = unlist(grp2$getConditions()), nrProteins= NAinfo)
+NAinfo <- data.frame(name = unlist(grp2$getConditions()), nrProteins = NAinfo)
```
```{r referencingChildDocument}
-child_docs <- "Grp2Analysis_MissingInOneCondition.Rmd_t"
-if(!sum(NAinfo$nrProteins > 0) > 0){
- child_docs <- "Grp2Analysis_Empty.Rmd_t"
+missingInOne <- "Grp2Analysis_MissingInOneCondition.Rmd"
+if (!sum(NAinfo$nrProteins > 0) > 0) {
+ missingInOne <- "Empty.Rmd"
}
+print(missingInOne)
+
```
-```{r includeMissingInOne, child = child_docs}
+```{r includeMissingInOne, child = missingInOne}
```
# Data Interpretation