priorDbParams: Class '"priorDbParams"'

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

Description

The main parameter class for HitWalker that controls how the prioritization via RWR is performed. This class will facilitate adapting this package for alternative uses and/or databases though once set appropriately can be mostly left alone by end users. Not all slots and retrieval methods will be applicable to all deployments and can be removed or addition ones added.

Objects from the Class

Objects can be created by calls of the form new("priorDbParams", ...). With the slots described in the below section as the arguments in lieu of '....'

Slots

id.table:

Object of class "character" Name of database table containing the sample information

possible.id.cols:

Object of class "character" Columns containing the possible ID values supplied by the user

reconciled.id.col:

Object of class "character" If a match is found, the column containing the human interpretable name

sample.id.col:

Object of class "character" If a match is found, the column containing the database ID

variant.query:

Object of class "function" Function that returns a suitable query for retrieving variant information

query.params:

Object of class "list" A list containing additional input needed by any functions with access to a priorDbParams object

filter.values:

Object of class "variantFilter" A variant filter object

matrix.query:

Object of class "function" Function resulting in an SQL query used to create the association graph

hit.query:

Object of class "function" Function resulting in an SQL query used to retrieve hit (e.g. functional assay) data

graph.trans.func:

Object of class "function" Function used to transform an association matrix into one of types used for input into an RWR algorithm

annot.query.func:

Object of class "function" Function resulting in an SQL query used to retrieve annotation for an annotatedIGraph object

score.summary.func:

Object of class "function" Function used to combine multiple functional hit score columns into a summary score

node.weight.col:

Object of class "character" Column from the resulting association graph (in FT form) from matrix.query used as a weight

patient.overlay.func:

Object of class "function" Function resulting in an SQL query retrieving the patient-specific metadata

seed.label:

Object of class "character" Value indicating how the functional assay hits should be referred to in the downstream functions

query.label:

Object of class "character" Value indicating how the variants should be referred to in the downstream functions

core.id:

Object of class "character" Columns in the SQL-derived data.frames that refer to the core IDs (i.e. those corresponding to nodes in the graph)

summary.id:

Object of class "character" Columns in the SQL-derived data.frames that refer to the summary IDs (e.g. gene symbol or Ensembl gene ID)

func.summary.map:

Object of class "character" A named character vector indicating whether the specified function uses a core or summary ID

hit.comb.score.name:

Object of class "character" Column that will be added to the hit SQL query result data.frame, indicating the summarized score if applicable

pat.freq.col:

Object of class "character" Column indicating the number of patients with a particular allele for a given variant in the variant SQL result data.frame

filter.col:

Object of class "character" Column in the variant SQL result data.frame that indicates a QA/QC filter for the given variant

variant.type.col:

Object of class "character" Column in the variant SQL result data.frame that indicates the type of variant (e.g. SNV, INDEL)

rwr.params:

Object of class "rwrParams" Parameter object controlling the RWR algorithm

additional.annot.ids:

Object of class "character" Additional IDs provided in the annotatedIGraph object that should be used in downstream functions

pat.var.id:

Object of class "character" The column in the retrieved variant data.frame that uniquely identifies the variants for each patient

verbose:

Object of class "logical" Indicates whether additional output should be printed in downstream functions

Methods

Convenience methods that retrieve data from the indicated slots of the variantFilter object contained in a priorDbParams object.

getFilterBestCategory

signature(obj = "priorDbParams")

getFilterCategory

signature(obj = "priorDbParams")

getFilterCollapseCol

signature(obj = "priorDbParams")

getFilterIgnoreCol

signature(obj = "priorDbParams")

getFilterLabels

signature(obj = "priorDbParams")

getFilterSep

signature(obj = "priorDbParams")

getFilterValues

signature(obj = "priorDbParams")

Retrieval and replacemement methods for the indicated slots for a priorDbParams object.

patVarID

signature(obj = "priorDbParams")

patVarID<-

signature(obj = "priorDbParams")

additionalIDs

signature(obj = "priorDbParams")

additionalIDs<-

signature(obj = "priorDbParams")

annotQuery

signature(obj = "priorDbParams")

annotQuery<-

signature(obj = "priorDbParams")

combScoreName

signature(obj = "priorDbParams")

combScoreName<-

signature(obj = "priorDbParams")

coreID

signature(obj = "priorDbParams")

coreID<-

signature(obj = "priorDbParams")

hitQuery

signature(obj = "priorDbParams")

hitQuery<-

signature(obj = "priorDbParams")

idTable

signature(obj = "priorDbParams")

idTable<-

signature(obj = "priorDbParams")

matrixQuery

signature(obj = "priorDbParams")

matrixQuery<-

signature(obj = "priorDbParams")

patientFilterCol

signature(obj = "priorDbParams")

patientFilterCol<-

signature(obj = "priorDbParams")

patientFreqCol

signature(obj = "priorDbParams")

patientFreqCol<-

signature(obj = "priorDbParams")

patientOverlay

signature(obj = "priorDbParams")

patientOverlay<-

signature(obj = "priorDbParams")

possibleIdCols

signature(obj = "priorDbParams")

possibleIdCols<-

signature(obj = "priorDbParams")

queryLabel

signature(obj = "priorDbParams")

queryLabel<-

signature(obj = "priorDbParams")

reconciledIdCol

signature(obj = "priorDbParams")

reconciledIdCol<-

signature(obj = "priorDbParams")

rwrParamsObj

signature(obj = "priorDbParams")

rwrParamsObj<-

signature(obj = "priorDbParams")

sampleIdCol

signature(obj = "priorDbParams")

sampleIdCol<-

signature(obj = "priorDbParams")

seedLabel

signature(obj = "priorDbParams")

seedLabel<-

signature(obj = "priorDbParams")

getSummarizationLevel

signature(obj = "priorDbParams")

summaryID

signature(obj = "priorDbParams")

summaryID<-

signature(obj = "priorDbParams")

summaryMap

signature(obj = "priorDbParams")

summaryMap<-

signature(obj = "priorDbParams")

variantFilterObj

signature(obj = "priorDbParams")

variantFilterObj<-

signature(obj = "priorDbParams")

variantQuery

signature(obj = "priorDbParams")

variantQuery<-

signature(obj = "priorDbParams")

variantTypeCol

signature(obj = "priorDbParams")

variantTypeCol<-

signature(obj = "priorDbParams")

nodeWeightCol

signature(obj = "priorDbParams")

show

signature(object = "priorDbParams")

transformGraph

signature(obj = "priorDbParams")

transformGraph<-

signature(obj = "priorDbParams")

verbLevel

signature(obj = "priorDbParams")

verbLevel<-

signature(obj = "priorDbParams")

queryParams

signature(obj = "priorDbParams")

queryParams<-

signature(obj = "priorDbParams")

scoreSummaryFunc

signature(obj = "priorDbParams")

scoreSummaryFunc<-

signature(obj = "priorDbParams")

Author(s)

Daniel Bottomly

See Also

variantFilter, rwrParams, run.prioritization.patient, variantPriorResult

Examples

param.obj <- HitWalker:::testPriorDbParams()

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