variantPriorResult: Class '"variantPriorResult"'

In dbottomly/HitWalker: Network-based variant prioriziation using functional assay scores

Description

Contains the results from a variant prioritization run for a single sample for additional summarization and/or analysis.

Objects from the Class

Objects can be created by calls of the form makeVariantPriorResult(prox.dta, graph, sample, var.dta, hit.dta, param.obj, prox.summary.id, var.summary.id, hit.summary.id, prox.rank.col, prox.type.col). Or equivalently through new("variantPriorResult", ...)

The end user should not need to instantiate an object of this class directly, instead one will be created from a call to run.prioritization.patient.

Slots

prox.dta:

Object of class "data.frame" containing the results from a RWR run produced from run.protocol.

graph:

Object of class "annotatedIGraph"

var.dta:

Object of class "data.frame" as created by a call to get.sample.variants.

hit.dta:

Object of class "data.frame" as created by a call to get.hit.prots.

sample:

Object of class "character" containing the sample name

param.obj:

Object of class "priorDbParams"

prox.summary.id:

Object of class "character" containing the summary ID used in creating the prox.dta data.frame.

var.summary.id:

Object of class "character" containing the summary ID used in creating the variant data.frame.

hit.summary.id:

Object of class "character" containing the summary ID used in creating the hit data.frame.

prox.rank.col:

Object of class "character" containing the column in prox.dta containing the rank of the nodes.

prox.type.col:

Object of class "character" containing the column in prox.dta containing the type of node (i.e. seed vs query) as named in priorDbParams.

Methods

Specific methods used for plotting, all of these have three additional arguments that need to be supplied:

node.names: A character vector of summary IDs named by the core IDs targ.nodes: The node names of the subgraph created from make.target.graph graph.param: A graphDispParams object

All return named character vectors.

getBestVarText

signature(obj = "variantPriorResult"): Retrieve node text for the representative variant of each node. The variant is chosen for the variant summary ID based on patient cohort frequency and quality filter as specified in the variantFilter object. The information that is displayed is controlled through the label.func.list slot in graphDispParams.

getBordColors

signature(obj = "variantPriorResult"): Retrieve border colors for the nodes. By default borders are black, see getFillColors below for an example of how to color borders based on node-specific data in the supplied objects.

getFillColors

signature(obj = "variantPriorResult"): Retrieve the fill colors for the nodes. By default nodes are colored based on whether they are a seed or query with coloring based on multiple categories being supported.

getNodeShapes

signature(obj = "variantPriorResult"): Retrieve node shapes as specified in the getShapeFunc method of graphDispParams and the process.node.annot function.

getNodeStyles

signature(obj = "variantPriorResult"): Retrieve node border styles (as in the lty graphical parameter) as specified in the getStyleFunc method of graphDispParams and the process.node.annot function.

General methods that access the specified slots

getGraph

signature(obj = "variantPriorResult")

getHitDta

signature(obj = "variantPriorResult")

getHitSummaryID

signature(obj = "variantPriorResult")

getParameters

signature(obj = "variantPriorResult")

getProxDta

signature(obj = "variantPriorResult")

getProxRankCol

signature(obj = "variantPriorResult")

getProxSummaryID

signature(obj = "variantPriorResult")

getProxTypeCol

signature(obj = "variantPriorResult")

getSampleName

signature(obj = "variantPriorResult")

getVarDta

signature(obj = "variantPriorResult")

getVarSummaryID

signature(obj = "variantPriorResult")

Methods that summarize data

summary

signature(object = "variantPriorResult"): Produces a merged data.frame summary of the prioritization. Desired columns can be specified as arguments.

plot

signature(object="variantPriorResult"): Produces a plot of the results. In order to modify the graphical parameters, a graphDispParams object and/or values corresponding to the slots of the object can be supplied

getProteinScores

signature(obj = "variantPriorResult"): Retrieves a data.frame of the hit scores used for prioritization ordered by score. There are two columns, the hit summary ID and summary score column specified in priorDbParams.

getRankedQueries

signature(obj = "variantPriorResult"): Retrieves an ordered data.frame of prioritization ranks. There are two columns, the prioritization summary ID and the rank column specified in priorDbParams.

Author(s)

Daniel Bottomly

See Also

graphDispParams, priorDbParams, make.target.graph, process.node.annot

Examples

if(require(RSQLite) && require(HitWalkerData))
{
	data(params)
	db.con <- dbConnect("SQLite", hitwalker.db.path())
	graph.obj <- loadGraph(graph.file.path(), examp.prior.param)
	test.out <- run.prioritization.patient(db.con=db.con, sample.id="08-00102", graph.obj=graph.obj, param.obj=examp.prior.param)
	head(summary(test.out))
}

dbottomly/HitWalker documentation built on May 15, 2019, 1:22 a.m.