\name{mirnapath-class}
\docType{class}
\alias{mirnapath-class}
\alias{show,mirnapath-method}
\title{ S4 class mirnapath and its "show" method }
\description{ miRNApath class intended to contain miRNA data,
gene and pathway associations, and ultimately the pathway
enrichment results in detail. }
\section{Objects from the Class}{
Objects can be created by calls of the form \code{new("mirnapath", ...)}.
}
\section{Slots}{
\describe{
\item{ \code{mirnaTable}:}{
Object of class \code{"data.frame"},
containing the miRNA results data, expected to
contain columns with miRNA name, gene name, and ideally
some column(s) for filtering hits versus background, e.g.
fold change, expression abundance, P-value. Once the data
is filtered (see state below) there will be a column with
a flag indicating which entries are hits and which are
considered background. This column is found in
\code{mirnaobj@columns["filterflagcolumn"]} and is typically
\code{"FILTERFLAG"}.
}
\item{ \code{columns}:}{
Object of class \code{"character"},
Named list of column headers used throughout the analysis.
The purpose of the names is partly to retain the original
headers in the mirnaTable data.frame, and partly to
coordinate the names with the miRNA-gene and gene-pathway
tables used later in the analysis. The recognized headers:
\code{mirnacol, assayidcol, genecol, pvaluecol, foldchangecol,
pathwaycol, pathwayidcol, groupcol, mirnagene}. See the
documentation for the mirnapath object type for more
details about usage.
}
\item{ \code{groupcount}:}{
Object of class \code{"numeric"},
indicating how many sample groups are
available in the data, provided for convenience.
}
\item{ \code{state}:}{
Object of class \code{"character"},
indicating the current analysis state,
with values: \code{"unfiltered"} if results are loaded but not
yet filtered; \code{"filtered"} if results are loaded and hits
are defined with the filterflagcol column; \code{"enriched"} if
the data is loaded, filtered, and analyzed for enrichment.
One can load mirna-gene and gene-pathway data at any point
which necessitates using the \code{mirnaobj@mirnaGene} or
\code{mirnaobj@mirnaPathways} object elements to determine if
that data has been loaded.
}
\item{ \code{mirnaGene}:}{
Object of class \code{"data.frame"},
containing associations between miRNA and
genes. The data should contain one miRNA-to-gene
relationship per row, and should contain only those two
columns. Additional columns are maintained but ignored.
Note that one can use any values in the genecol column,
provided they match exactly with values found in the
\code{mirnaobj@mirnaPathways} element (see below.) Therefore,
if desired one can use transcript or gene associations,
or other integration methods as desired.
}
\item{ \code{mirnaPathways}:}{
Object of class \code{"data.frame"},
containing gene-pathway associations. The data
should contain only one gene-to-pathway association per
row of data. The data can have pathway ID values, which
may facilitate comparisons to pathway databases (and may
allow substantial data volume reduction if necessary.) If
there is no pathwayidcol column, then one will be created
using a numerical assignments of the pathway names. Note
that this conversion is not sensitive to pathway sources,
so care should be taken to include pathway source in the
pathway name if two sources share the same pathway name.
The same is true for pathway ID values, should they be
purely numerical and have shared values across pathway
sources.
}
\item{ \code{pathwaycount}:}{
Object of class \code{"numeric"},
Numerical value indicating how many pathways are
available in the data, provided for convenience.
}
\item{ \code{filters}:}{
Object of class \code{"numeric"},
List of filters applied to the data, which may include:
\code{"P-value", "Fold change"}, and/or \code{"Expression"}.
}
\item{ \code{enrichment}:}{
Enrichment summary data in the form of a list of elements
for each sample group (the sample group is the name of
each element.) Each list element is itself a list with
enrichment result data for each sample group, as
independently calculated: \code{"pvalues"} - list of P-values
named by pathway ID; \code{"Measured pathway mirnaGenes"} -
total number of miRNA-gene-pathway combinations measured,
which gives some idea of the overall coverage of pathways.
The general point is that miRNAs have the potential to
cover many genes and pathways; \code{"Total mirnaGenes"} - number
of miRNA-gene combinations represented in the data;
\code{"Enriched pathway mirnaGenes"} - number of miRNA-gene values
enriched in the pathway tested; \code{"Enriched by miRNA"} - list
of miRNAs involved in the pathway tested, with the list of
genes in parentheses per miRNA; \code{"Enriched by Gene"} - same
as previous except switching gene and miRNA; \code{"Total
enriched mirnaGenes"} - the total number of miRNA-gene
values involved in any pathway enrichment (significant or
not.) The total values are useful when comparing across
sample groups, looking particularly for groups with few
changes or those with a uniquely high number of changes.
}
\item{ \code{pathwayList}:}{
Object of class \code{"character"}, pathways contained in the
\code{mirnaobj@mirnaPathways} object, named by the pathway ID
values found in the pathwayidcol column. This list
facilitates converting the data in the enrichment element
to pathway names, since those values are named by the
pathway ID to conserve memory.
}}
}
\section{Methods}{
\describe{
\item{show}{\code{signature(object = "mirnapath")}: ... }
}
}
\source{
Journal of Alzheimers Disease 14, 27-41.
}
\references{
John Cogswell (2008) Identification of miRNA changes
in Alzheimer's disease brain and CSF yields putative
biomarkers and insights into disease pathways, Journal of
Alzheimer's Disease 14, 27-41.
}
\examples{
library(miRNApath);
data(mirnaobj);
# the slotNames and definitions are described
#showClass(mirnaobj);
# Default "show" method describes the contents of the object
mirnaobj;
}
\keyword{classes}