csSpecificity

Description

Returns a matrix of 'Specificity scores' (S) defined as 1-JSD(p_g,q_i) where p_g is the Log10+1 expression profile of a gene g across all conditions j, collapsed into a probability distribution, and q_i is the unit vector of 'perfect expression' in a given condition i.

Usage

## S4 method for signature 'CuffFeatureSet'
csSpecificity(object,logMode=T,pseudocount=1,relative=FALSE,...)
## S4 method for signature 'CuffData'
csSpecificity(object,logMode=T,pseudocount=1,relative=FALSE,...)

Arguments

Details

None

Author(s)

Loyal A. Goff

Source

None

References

None.

Examples

	data(sampleData)
	csSpecificity(sampleGeneSet)

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)

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Type 'license()' or 'licence()' for distribution details.

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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(cummeRbund)
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: RSQLite
Loading required package: DBI
Loading required package: ggplot2
Loading required package: reshape2
Loading required package: fastcluster

Attaching package: 'fastcluster'

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

    hclust

Loading required package: rtracklayer
Loading required package: GenomicRanges
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

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

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Gviz
Loading required package: grid

Attaching package: 'cummeRbund'

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

    promoters

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

    promoters

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

    conditions

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/cummeRbund/csSpecificity.Rd_%03d_medium.png", width=480, height=480)
> ### Name: csSpecificity
> ### Title: csSpecificity
> ### Aliases: csSpecificity csSpecificity,CuffFeatureSet-method
> ###   csSpecificity,CuffData-method
> ### Keywords: datasets
> 
> ### ** Examples
> 
> 	data(sampleData)
> 	csSpecificity(sampleGeneSet)
Using tracking_id, sample_name as id variables
             iPS_spec    hESC_spec Fibroblasts_spec
XLOC_000069 0.3404865 5.281363e-01       0.03949159
XLOC_000089 0.2843602 3.315380e-01       0.35041646
XLOC_000105 0.3006743 3.138327e-01       0.35217793
XLOC_000115 1.0000000 0.000000e+00       0.00000000
XLOC_000132 0.2940644 3.073414e-01       0.36481155
XLOC_000151 0.4977991 3.247807e-01       0.11444635
XLOC_000158 0.2405263 6.483151e-01       0.00000000
XLOC_000170 0.2102559 5.488920e-01       0.18734324
XLOC_001240 0.3011602 3.143650e-01       0.35118948
XLOC_001262 0.2809749 3.504865e-01       0.33471435
XLOC_001263 0.2832491 3.344485e-01       0.34859109
XLOC_001265 0.2596253 3.892470e-01       0.31531604
XLOC_001297 0.0000000 3.416102e-01       0.54346293
XLOC_001339 0.3365391 3.265969e-01       0.30384333
XLOC_001348 0.7079814 1.110223e-16       0.18534248
XLOC_001359 0.3093951 3.090976e-01       0.34833884
XLOC_001363 1.0000000 0.000000e+00       0.00000000
XLOC_001369 0.3222189 3.274421e-01       0.31750748
XLOC_001370 0.2880325 3.117768e-01       0.36625945
XLOC_001411 0.3426006 3.485996e-01       0.27467945
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>