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")
Results
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(GGtools)
Loading required package: GGBase
Loading required package: snpStats
Loading required package: survival
Loading required package: Matrix
Loading required package: data.table
Loading required package: parallel
Loading required package: Homo.sapiens
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
rbind, rownames, sapply, setdiff, sort, table, tapply, union,
unique, unsplit
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: IRanges
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following objects are masked from 'package:Matrix':
colMeans, colSums, expand, rowMeans, rowSums
The following objects are masked from 'package:base':
colMeans, colSums, expand.grid, rowMeans, rowSums
Attaching package: 'IRanges'
The following object is masked from 'package:data.table':
shift
Loading required package: OrganismDbi
Loading required package: GenomicFeatures
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: GO.db
Loading required package: org.Hs.eg.db
Loading required package: TxDb.Hsapiens.UCSC.hg19.knownGene
Attaching package: 'GGtools'
The following object is masked from 'package:stats':
getCall
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/GGtools/EqAppr-class.Rd_%03d_medium.png", width=480, height=480)
> ### Name: EqAppr-class
> ### Title: Class '"EqAppr"'
> ### Aliases: EqAppr-class calfig,EqAppr,character-method
> ### getModnames,EqAppr-method getPruned,EqAppr-method
> ### getSens,EqAppr-method getUnpruned,EqAppr-method show,EqAppr-method
> ### show,ApprRes-method calfig
> ### Keywords: classes
>
> ### ** Examples
>
> showClass("EqAppr")
Class "EqAppr" [package "GGtools"]
Slots:
Name: meta sens pruned unpruned
Class: ApprMeta ApprSens ApprRes ApprRes
>
>
>
>
>
> dev.off()
null device
1
>
providing 
.