PathSummaryRunner-class: PathSummaryRunner

In biodev/packageDir: Tool for in silico functional analysis design and exploration of relation between genomic function and aberration.

Description

This reference class object is used in the pathway analysis. It provides all available data for internal functions and user-defined functions to conduct pathway analysis.

Fields

patientGeneMatrix:

Object of class "Matrix" Bipartate graph with patient ids as columns, genes as rows and values, logical indicating if gene is 'active' (drug sensitive, aberrational, etc.) in patient.

coverage_summary:

Object of class "list" Same data as is found in [[result]] set, only filled if analysis platform in question is coverage-limited, ie, coverage slot of PathSummaryRunner is filled.

coverage:

Object of class "Character" A character vector containing symbols for the set of species (ie genes) covered by the analysis platform. If this is provided, pathway analysis will be limited to included only genes in the coverage set. This should be provided if an analysis platform is not considered to have full-genome coverage (ex: sequence capture data for 3000 unique genes.).

indPatientSummarySettings:

Object of class "list" Settings object for analysis of individual patients (as opposed to a full cohort).

original_data_matrix:

Object of class "matrix" The original, untransformed data set.

min_gene_frequency:

Object of class "numeric" The minimum frequency across the cohort for a gene to be considered as active (aberrational, drug sensitive, etc..) in the pathway analysis. (default 0 imposes no threshold)

min_gene_count:

Object of class "numeric" Analogous to min_gene_frequency – the minimum number of patients with gene in active state for it to be considered active in the pathway analysis. (default 1 imposes no threshold)

individualEnrichment:

Object of class "logical" A flag indicating if path analysis should be run for individual patients. (note, if individual patient analysis is run, min_gene_frequency and min_gene_count will automatically be set to 0 and 1, respectively, in the analysis of individual patients (though will be maintained in the analysis of any full cohort))

.verbose:

Object of class "logical" Flag indicating if extra output should be shown.

.significanceTests:

Object of class "list" Each slot contains a function. Each function implements the path test interface, accepting a PathSummaryRunner as an input, and returning a data frame with path names or identifiers as row names and values indicating pathway's significance (ex: p-values).

settings:

Object of class "list" The settings list object.

targetname:

Object of class "character" One word description of the genes affected (ex: mutated)

dataSetName:

Object of class "character" Description of the data set analyzed by the current arm.

study:

Object of class "Study" The study object for the current analysis.

.targetMatrix:

Object of class "matrix" Bipartate graph matrix. This is a version of the pathway bipartate graph reduced to only contain genes considered "active" (aberrational or functionally sensitive). This is the primary matrix used in computing pathway significance.

patientsum:

Object of class "matrix" Numeric values indicating the number of genes affected in each patient. Patient IDs are given as row names, values are the number of genes affected in each patient.

path_summary_each_patient:

Object of class "list" The results sets for each patient. List names are set as patient identifiers.

gene_count_matrix:

Object of class "matrix" Values are "numeric" Row names are gene identifiers. Values are the number of patients with affected gene.

.gene_frequency_matrix:

Object of class "matrix" The frequency across cohort that each gene is active.

.gene_vector:

Object of class "matrix" Gene identifiers are given as row names. Values are logical, indicating if genes are considered 'active' in current cohort (or patient, for individual patient analysis).

genomicnotpw:

Object of class "matrix" Values are "character" identifiers for affected genes not found in pathways.

active_genes_ea_path:

Object of class "matrix" Values are pasted together "character" vectors of identifiers for genes found active in each pathway. Row names are given as pathway identifiers.

pathsummary:

Object of class "data.frame" containing main coverage and enrichment summary data for each affected pathway.

biodev/packageDir documentation built on Nov. 4, 2019, 7:19 a.m.