EqAppr-class: Class '"EqAppr"'

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

Description

Manage the appraisal of an eQTL search

Objects from the Class

Objects can be created by calls of the form new("EqAppr", ...), or via buildEqAppr()

Slots

meta:

Object of class "ApprMeta" basic descriptive information about source analysis

sens:

Object of class "ApprSens" outputs of sensitivity analysis

pruned:

Object of class "ApprRes" outputs of appraisal for LD-pruned predictions

unpruned:

Object of class "ApprRes" outputs of general appraisal without LD pruning

Methods

calfig

signature(x = "EqAppr", ind = "character"): Additional arguments can be specified:

ind

index or name of model to be plotted

hfudgetxt

distance to move rendered fractions relative to bin x coordinate

tickend

maximum value at which axis tick mark will be plotted

tickgap

axis will have ticks at seq(0, tickend, tickgap)

ylimin

ylim setting for rendering

xlimin

xlim setting for rendering

fraccex

cex setting for fraction rendering

fuselast

if data are sparse in entries of high predicted probability, you can fuse the nearby cells up to the end – pick fuselast=2 for final 2 cells, 3 for final 3 and so on

getModnames

signature(x = "EqAppr"): obtain the list of strings used to name different appraisal models

getPruned

signature(x = "EqAppr"): get the ApprRes instance corresponding to the LD-pruned loci

getUnpruned

signature(x = "EqAppr"): get the ApprRes instance for all loci in use

getSens

signature(x = "EqAppr"): get sensitivity analysis results

show

signature(object = "EqAppr"): concise report

Examples

showClass("EqAppr")

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