sensiCisInput-class: Class '"sensiCisInput"'

In GGtools: software and data for analyses in genetics of gene expression

Description

Manage references to collections of cis-eQTL searches for sensitivity analysis.

Objects from the Class

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

Slots

cisMgrFiles:

Object of class "character": a vector of filenames, each file is an instance of class mcwBestCis-class

cisMgrProperties:

Object of class "list" one vector with named elements per element of cisMgrFiles, with components rad, excl, maf, nperm, npc; see details below.

probeannopk:

Object of class "character", identifying a bioconductor probe annotation package that can be used to map probe identifiers to other vocabularies or feature value sets

Methods

sensanal

signature(object = "sensiCisInput", fdrbound = "numeric"): generates an instance of sensiCisOutput-class with summarization of sensitivities

show

signature(object = "sensiCisInput"): concise rendering

Note

This version of sensitivity analysis support is rudimentary and involves manual construction of metadata that should be extractable from analysis outputs. The radius of the cis search (and radius of excluded interior if used) are identified as elements named rad and excl in the cisMgrProperties vectors; additional elements maf, nperm, and npc define the lower bound for minor allele frequency, number of permutations for plug-in FDR computation, and number of principal components removed to adjust for expression heterogeneity in the associated cis-eQTL search.

Examples

showClass("sensiCisInput")

GGtools documentation built on Nov. 8, 2020, 6:32 p.m.