mirnapath-class: S4 class mirnapath and its "show" method

In miRNApath: miRNApath: Pathway Enrichment for miRNA Expression Data

Description

miRNApath class intended to contain miRNA data, gene and pathway associations, and ultimately the pathway enrichment results in detail.

Objects from the Class

Objects can be created by calls of the form new("mirnapath", ...).

Slots

mirnaTable:

Object of class "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 mirnaobj@columns["filterflagcolumn"] and is typically "FILTERFLAG".

columns:

Object of class "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: mirnacol, assayidcol, genecol, pvaluecol, foldchangecol, pathwaycol, pathwayidcol, groupcol, mirnagene. See the documentation for the mirnapath object type for more details about usage.

groupcount:

Object of class "numeric", indicating how many sample groups are available in the data, provided for convenience.

state:

Object of class "character", indicating the current analysis state, with values: "unfiltered" if results are loaded but not yet filtered; "filtered" if results are loaded and hits are defined with the filterflagcol column; "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 mirnaobj@mirnaGene or mirnaobj@mirnaPathways object elements to determine if that data has been loaded.

mirnaGene:

Object of class "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 mirnaobj@mirnaPathways element (see below.) Therefore, if desired one can use transcript or gene associations, or other integration methods as desired.

mirnaPathways:

Object of class "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.

pathwaycount:

Object of class "numeric", Numerical value indicating how many pathways are available in the data, provided for convenience.

filters:

Object of class "numeric", List of filters applied to the data, which may include: "P-value", "Fold change", and/or "Expression".

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: "pvalues" - list of P-values named by pathway ID; "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; "Total mirnaGenes" - number of miRNA-gene combinations represented in the data; "Enriched pathway mirnaGenes" - number of miRNA-gene values enriched in the pathway tested; "Enriched by miRNA" - list of miRNAs involved in the pathway tested, with the list of genes in parentheses per miRNA; "Enriched by Gene" - same as previous except switching gene and miRNA; "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.

pathwayList:

Object of class "character", pathways contained in the 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.

Methods

show

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;

Example output

mirnapath object:
   Length     Class      Mode 
        1 mirnapath        S4 

Columns specified:
   mirnacol = "miRNA Name"
   assayidcol = "ASSAYID"
   groupcol = "GROUP"
   filterflagcol = "FILTERFLAG"
   mirnagene = "miRNA-Gene"
   genecol = "Entrez Gene ID"
   pathwaycol = "Pathway Name"
   pathwayidcol = "PATHWAY_ID"
   pvaluecol = "P-value"
   
Filters Applied:
   none

Number of miRNAs: 196 
Number of sample groups: 18 
Number of pathways: 771 
State: filtered 

miRNApath documentation built on Nov. 8, 2020, 4:52 p.m.