EqAppr-class {GGtools} | R Documentation

## Class `"EqAppr"`

### 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")

[Package GGtools version 5.25.3 Index]