annot_KinSub.Rd

% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/kin.R
\name{annot_KinSub}
\alias{annot_KinSub}
\title{Annotates kinase-substrate interactions}
\usage{
annot_KinSub(df, db_nms, match_orgs, id, filepath = NULL, filename = NULL, ...)
}
\arguments{
\item{df}{The name of a primary data file. By default, it will be determined
automatically after matching the types of data and analysis with an
\code{id} among \code{c("pep_seq", "pep_seq_mod", "prot_acc", "gene")}. A
primary file contains normalized peptide or protein data and is among
\code{c("Peptide.txt", "Peptide_pVal.txt", "Peptide_impNA_pVal.txt",
"Protein.txt", "Protein_pVal.txt", "protein_impNA_pVal.txt")}. For analyses
require the fields of significance p-values, the \code{df} will be one of
\code{c("Peptide_pVal.txt", "Peptide_impNA_pVal.txt", "Protein_pVal.txt",
"protein_impNA_pVal.txt")}.}

\item{db_nms}{Character string(s) to the name(s) of PSP database(s) with
prepended directory path(s). Users need to download the kinase-substrate
table, e.g. \code{Kinase_Substrate_Dataset.txt} directly from the PSP
website and supply the corresponding file path(s) and name(s). Currently
assume single database file.}

\item{match_orgs}{Logical; if TRUE, matches the organism between kinases and
their acting substrates. The default is TRUE.}

\item{id}{Character string; one of \code{pep_seq}, \code{pep_seq_mod},
\code{prot_acc} and \code{gene}.}

\item{filepath}{A file path to output results. By default, it will be
determined automatically by the name of the calling function and the value
of \code{id} in the \code{call}.}

\item{filename}{A representative file name to outputs. By default, the
name(s) will be determined automatically. For text files, a typical file
extension is \code{.txt}. For image files, they are typically saved via
\code{\link[ggplot2]{ggsave}} or \code{\link[pheatmap]{pheatmap}} where the
image type will be determined by the extension of the file name.}

\item{...}{\code{filter_}: Variable argument statements for the row
filtration of data against the column keys in \code{Peptide.txt} for
peptides or \code{Protein.txt} for proteins. Each statement contains to 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. \cr \cr For example,
\code{pep_len} is a column key in \code{Peptide.txt}. The statement
\code{filter_peps_at = exprs(pep_len <= 50)} will remove peptide entries
with \code{pep_len > 50}. See also \code{\link{normPSM}}. \cr \cr
Additional parameters for plotting with \code{ggplot2}: \cr \code{xmin},
the minimum \eqn{x} at a log2 scale; the default is -2. \cr \code{xmax},
the maximum \eqn{x} at a log2 scale; the default is +2. \cr \code{xbreaks},
the breaks in \eqn{x}-axis at a log2 scale; the default is 1. \cr
\code{binwidth}, the binwidth of \code{log2FC}; the default is \eqn{(xmax -
xmin)/80}. \cr \code{ncol}, the number of columns; the default is 1. \cr
\code{width}, the width of plot; \cr \code{height}, the height of plot. \cr
\code{scales}, should the scales be fixed across panels; the default is
"fixed" and the alternative is "free".}
}
\description{
Annotates kinase-substrate interactions
}