Determine the number of latent factors K.

Description

Determines the number of latent variables K via AIC, BIC, and deviance reduction. A pdf file containing all three plots is generated.

Usage

choiceofK(AIC, BIC, RSS, K, filename)

Arguments

Details

AIC: Akaike information criterion, used for model selection; BIC: Bayesian information criterion, used for model selection; RSS: residue sum of squares, used to plot scree plot and determine the 'elbow'.

Value

pdf file with three plots: AIC, BIC, and percentage of variance explained versus the number of latent factors.

Author(s)

Yuchao Jiang yuchaoj@wharton.upenn.edu

See Also

normalize, segment

Examples

AIC <- normObjDemo$AIC
BIC <- normObjDemo$BIC
RSS <- normObjDemo$RSS
K <- normObjDemo$K
projectname <- bambedObjDemo$projectname
chr <- bambedObjDemo$chr
choiceofK(AIC, BIC, RSS, K, filename = paste(projectname, "_", chr, 
    "_choiceofK", ".pdf", sep = ""))

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(CODEX)
Loading required package: Rsamtools
Loading required package: GenomeInfoDb
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

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: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: Biostrings
Loading required package: XVector
Loading required package: BSgenome.Hsapiens.UCSC.hg19
Loading required package: BSgenome
Loading required package: rtracklayer

Attaching package: 'CODEX'

The following object is masked from 'package:BiocGenerics':

    normalize

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/CODEX/choiceofK.Rd_%03d_medium.png", width=480, height=480)
> ### Name: choiceofK
> ### Title: Determine the number of latent factors K.
> ### Aliases: choiceofK
> ### Keywords: package
> 
> ### ** Examples
> 
> AIC <- normObjDemo$AIC
> BIC <- normObjDemo$BIC
> RSS <- normObjDemo$RSS
> K <- normObjDemo$K
> projectname <- bambedObjDemo$projectname
> chr <- bambedObjDemo$chr
> choiceofK(AIC, BIC, RSS, K, filename = paste(projectname, "_", chr, 
+     "_choiceofK", ".pdf", sep = ""))
png 
  2 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>