Pep2Prn.Rd

% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/peptable.R
\name{Pep2Prn}
\alias{Pep2Prn}
\title{Interim protein data}
\usage{
Pep2Prn(
  use_unique_pep = TRUE,
  impute_prot_na = FALSE,
  cut_points = Inf,
  rm_outliers = FALSE,
  rm_allna = FALSE,
  mc = TRUE,
  ...
)
}
\arguments{
\item{use_unique_pep}{Logical. If TRUE, only entries that are \code{TRUE} or
equal to \code{1} under the column \code{pep_isunique} in \code{Peptide.txt}
will be used, for summarizing the \code{log2FC} and the \code{intensity} of
peptides into protein values. The default is to use unique peptides only.
For \code{MaxQuant} data, the levels of uniqueness are according to the
\code{pep_unique_by} in \code{\link{normPSM}}. The argument currently do
nothing to \code{Spectrum Mill} data where both unique and shared peptides
will be kept.}

\item{impute_prot_na}{Logical; impute NA values of protein log2FC or not.}

\item{cut_points}{A named, numeric vector defines the cut points (knots) for
the median-centering of \code{log2FC} by sections. For example, at
\code{cut_points = c(mean_lint = seq(4, 7, .5))}, \code{log2FC} will be
binned according to the intervals of \eqn{-Inf, 4, 4.5, ..., 7, Inf} under
column \code{mean_lint} (mean log10 intensity) in the input data. The
default is \code{cut_points = Inf}, or equivalently \code{-Inf}, where the
\code{log2FC} under each sample will be median-centered as one piece. See
also \code{\link{prnHist}} for data binning in histogram visualization.}

\item{rm_outliers}{Logical; if TRUE, PSM outlier removals will be performed
for peptides with more than two identifying PSMs. Dixon's method will be
used when \eqn{2 < n \le 25} and Rosner's method will be used when \eqn{n >
25}. The default is FALSE.}

\item{rm_allna}{Logical; if TRUE, removes data rows that are exclusively NA
across ratio columns of \code{log2_R126} etc. The setting also applies to
\code{log2_R000} in LFQ.}

\item{mc}{Logical. At the TRUE default, performs median-centering of
\code{log2FC} after the peptide-to-protein aggregation. Otherwise, the
summarized \code{log2FC} values will be left as they are.}

\item{...}{\code{filter_}: Variable argument statements for the filtration of
data rows. Each statement contains a list of logical expression(s). The
\code{lhs} needs to start with \code{filter_}. The logical condition(s) at
the \code{rhs} needs to be enclosed in \code{exprs} with round parenthesis.
For example, \code{pep_len} is a column key in \code{Peptide.txt}. The
statement of \code{filter_peps_at = exprs(pep_len <= 50)} will remove
peptide entries with \code{pep_len > 50}.}
}
\value{
The primary output in "\code{.../Protein/Protein.txt}".
}
\description{
\code{Pep2Prn} summarizes \code{Peptide.txt} to an interim protein report in
\code{Protein.txt}.
}
\details{
Fields other than \code{log2FC} and \code{intensity} are summarized with
median statistics.
}
\examples{
\donttest{
# ===================================
# Peptides to proteins
# ===================================

## !!!require the brief working example in `?load_expts`

# use unique peptides
Pep2Prn()

# include shared peptides
Pep2Prn(use_unique_pep = FALSE)  

# alignment of data by segments
Pep2Prn(cut_points = seq(4, 7, 0.5))
}
}
\seealso{
\emph{Metadata} \cr \code{\link{load_expts}} for metadata preparation
 and a reduced working example in data normalization \cr

 \emph{Data normalization} \cr \code{\link{normPSM}} for extended examples in
 PSM data normalization \cr \code{\link{PSM2Pep}} for extended examples in
 PSM to peptide summarization \cr \code{\link{mergePep}} for extended
 examples in peptide data merging \cr \code{\link{standPep}} for extended
 examples in peptide data normalization \cr \code{\link{Pep2Prn}} for
 extended examples in peptide to protein summarization \cr
 \code{\link{standPrn}} for extended examples in protein data normalization.
 \cr \code{\link{purgePSM}} and \code{\link{purgePep}} for extended examples
 in data purging \cr \code{\link{pepHist}} and \code{\link{prnHist}} for
 extended examples in histogram visualization. \cr \code{\link{extract_raws}}
 and \code{\link{extract_psm_raws}} for extracting MS file names \cr

 \emph{Variable arguments of `filter_...`} \cr \code{\link{contain_str}},
 \code{\link{contain_chars_in}}, \code{\link{not_contain_str}},
 \code{\link{not_contain_chars_in}}, \code{\link{start_with_str}},
 \code{\link{end_with_str}}, \code{\link{start_with_chars_in}} and
 \code{\link{ends_with_chars_in}} for data subsetting by character strings
 \cr

 \emph{Missing values} \cr \code{\link{pepImp}} and \code{\link{prnImp}} for
 missing value imputation \cr

 \emph{Informatics} \cr \code{\link{pepSig}} and \code{\link{prnSig}} for
 significance tests \cr \code{\link{pepVol}} and \code{\link{prnVol}} for
 volcano plot visualization \cr \code{\link{prnGSPA}} for gene set enrichment
 analysis by protein significance pVals \cr \code{\link{gspaMap}} for mapping
 GSPA to volcano plot visualization \cr \code{\link{prnGSPAHM}} for heat map
 and network visualization of GSPA results \cr \code{\link{prnGSVA}} for gene
 set variance analysis \cr \code{\link{prnGSEA}} for data preparation for
 online GSEA. \cr \code{\link{pepMDS}} and \code{\link{prnMDS}} for MDS
 visualization \cr \code{\link{pepPCA}} and \code{\link{prnPCA}} for PCA
 visualization \cr \code{\link{pepLDA}} and \code{\link{prnLDA}} for LDA
 visualization \cr \code{\link{pepHM}} and \code{\link{prnHM}} for heat map
 visualization \cr \code{\link{pepCorr_logFC}}, \code{\link{prnCorr_logFC}},
 \code{\link{pepCorr_logInt}} and \code{\link{prnCorr_logInt}}  for
 correlation plots \cr \code{\link{anal_prnTrend}} and
 \code{\link{plot_prnTrend}} for trend analysis and visualization \cr
 \code{\link{anal_pepNMF}}, \code{\link{anal_prnNMF}},
 \code{\link{plot_pepNMFCon}}, \code{\link{plot_prnNMFCon}},
 \code{\link{plot_pepNMFCoef}}, \code{\link{plot_prnNMFCoef}} and
 \code{\link{plot_metaNMF}} for NMF analysis and visualization \cr

 \emph{Custom databases} \cr \code{\link{Uni2Entrez}} for lookups between
 UniProt accessions and Entrez IDs \cr \code{\link{Ref2Entrez}} for lookups
 among RefSeq accessions, gene names and Entrez IDs \cr \code{\link{prepGO}}
 for
 \code{\href{http://current.geneontology.org/products/pages/downloads.html}{gene
  ontology}} \cr \code{\link{prepMSig}} for
 \href{https://data.broadinstitute.org/gsea-msigdb/msigdb/release/7.0/}{molecular
  signatures} \cr \code{\link{prepString}} and \code{\link{anal_prnString}}
 for STRING-DB \cr

 \emph{Column keys in PSM, peptide and protein outputs} \cr
 system.file("extdata", "psm_keys.txt", package = "proteoQ") \cr
 system.file("extdata", "peptide_keys.txt", package = "proteoQ") \cr
 system.file("extdata", "protein_keys.txt", package = "proteoQ") \cr
}