toolsFactorizationClass {hapFabia} | R Documentation

## Tools to analyze results of fabia

### Description

These tools allow to analyze results of the package fabia. They can be used to identify IBD segment regions and for adjusting the parameters of `extractIBDsegments` and `hapFabia` such as `ps` (top L values for extraction), `psZ` (top Z values for extraction), `inteA` (length of histogram bins).

`plotL` plots the loadings of a fabia result that are above a threshold either as points, histogram or by a smooth scatter plot.

`topLZ` returns largest L or Z values of a fabia result, where thresholds are given either by a quantile or by a value.

`histL` supplies a histogram of the loadings obtained by fabia.

### Usage

    plotL(res,n=1,p=NULL,w=NULL,type="points",
       intervv=500,off=0,t="p",cex=1)

    histL(res,n=1,p=NULL,w=NULL,intervv=500,off=0)

    topLZ(res,n=1,LZ="L",indices=TRUE,p=NULL,w=NULL)

### Arguments

`res` | fabia result; instance of the class `Factorization`.
`n` | the number of the bicluster to consider.
`p` | the quantile threshold above which values are returned (p or w must be given).
`w` | the value threshold above which values are returned (p or w must be given).
`type` | the type of the plot: `type=c("points","histogram","smoothScatter")`.
`intervv` | length of the interval bins for histograms.
`off` | offset of the interval bins from zero for histograms.
`t` | points type for the plot.
`cex` | size of the points for the plot.
`LZ` | "L" for loadings L or "Z" for factors Z.
`indices` | if `TRUE` (default) indices are given and otherwise values.

### Details

`plotL` plots the loadings of a fabia result that are above a threshold either as points, histogram or by a smooth scatter plot. Thresholds can be given by a quantile or by a value.

`topLZ` returns largest L or Z indices/values of a fabia result. Thresholds are given by quantile or by a value.

`histL` computes histogram of the loadings obtained by fabia.

Implementation in R.

### Value

`` | `plotL`: nothing.
`` | `topLZ`: vector of indices or values depending on the logical parameter indices.
`` | `histL`: object of class `histogram`.

### Author(s)

Sepp Hochreiter

### References

S. Hochreiter et al., ‘FABIA: Factor Analysis for Bicluster Acquisition’, Bioinformatics 26(12):1520-1527, 2010.

### See Also

`IBDsegment-class`, `IBDsegmentList-class`, `analyzeIBDsegments`, `compareIBDsegmentLists`, `extractIBDsegments`, `findDenseRegions`, `hapFabia`, `hapFabiaVersion`, `hapRes`, `chr1ASW1000G`, `IBDsegmentList2excel`, `identifyDuplicates`, `iterateIntervals`, `makePipelineFile`, `matrixPlot`, `mergeIBDsegmentLists`, `mergedIBDsegmentList`, `plotIBDsegment`, `res`, `setAnnotation`, `setStatistics`, `sim`, `simu`, `simulateIBDsegmentsFabia`, `simulateIBDsegments`, `split_sparse_matrix`, `toolsFactorizationClass`, `vcftoFABIA`

### Examples

    data(res)

    plotL(res,n=1,p=0.95,w=NULL,type="histogram",
       intervv=50,off=0,t="p",cex=1)
    plotL(res,n=1,p=0.95,w=NULL,type="points",
       intervv=50,off=0,t="p",cex=1)
    plotL(res,n=1,p=NULL,w=0.5,type="points",
       intervv=50,off=0,t="p",cex=1)
    plotL(res,n=1,p=0.95,w=NULL,type="smooth",
       intervv=50,off=0,t="p",cex=1)
    plotL(res,n=1,p=NULL,w=0.5,type="smooth",
       intervv=50,off=0,t="p",cex=1)

    topLZ(res,n=1,LZ="L",indices=TRUE,p=0.95,w=NULL)
    topLZ(res,n=1,LZ="L",indices=TRUE,p=NULL,w=0.95)

    topLZ(res,n=1,LZ="Z",indices=TRUE,p=0.95,w=NULL)
    topLZ(res,n=1,LZ="Z",indices=TRUE,p=NULL,w=0.4)

    topLZ(res,n=1,LZ="L",indices=FALSE,p=0.95,w=NULL)
    topLZ(res,n=1,LZ="L",indices=FALSE,p=NULL,w=0.95)

    topLZ(res,n=1,LZ="Z",indices=FALSE,p=0.95,w=NULL)
    topLZ(res,n=1,LZ="Z",indices=FALSE,p=NULL,w=0.4)

    h1 <- histL(res,n=1,p=0.9,w=NULL,intervv=50,off=0)
    print(h1$counts)
    h1 <- histL(res,n=1,p=NULL,w=0.5,intervv=50,off=0)
    print(h1$counts)

[Package hapFabia version 1.29.0 Index]