critical regions

Description

critical region cutpoints

Usage

  critVal.alpha(k, p0, alpha, posdiff)

Arguments

Details

This version uses alpha and will find TFD

Value

list of cutoffs and attributes

Author(s)

Charles Berry

See Also

gRxCluster for how and why this function is used

Examples

# symmetric odds:
crit <- critVal.alpha(5:25,c(1,1)/2,alpha=0.05,
                      matrix(1,nr=50,nc=21))
crit[[1]]
sapply(crit,c)
# 5:1 odds
asymmetric.crit <- critVal.alpha(5:25,c(1,5)/6,alpha=0.05,
                      matrix(1,nr=50,nc=21))
# show the critical regions
par(mfrow=c(1,2))
gRxPlot(crit,method="critical")
gRxPlot(asymmetric.crit,method="critical")
rm(crit,asymmetric.crit)

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 'demo()' for some demos, 'help()' for on-line help, or
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Type 'q()' to quit R.

> library(geneRxCluster)
Loading required package: GenomicRanges
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
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
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/geneRxCluster/critVal.alpha.Rd_%03d_medium.png", width=480, height=480)
> ### Name: critVal.alpha
> ### Title: critical regions
> ### Aliases: critVal.alpha
> 
> ### ** Examples
> 
> # symmetric odds:
> crit <- critVal.alpha(5:25,c(1,1)/2,alpha=0.05,
+                       matrix(1,nr=50,nc=21))
> crit[[1]]
low  up 
  0   6 
attr(,"fdr")
     target.low target.hi     low      hi
[1,]      3.125   100.000 0.03125 1.00000
[2,]     18.750    96.875 0.18750 0.96875
[3,]     50.000    81.250 0.50000 0.81250
[4,]     81.250    50.000 0.81250 0.50000
[5,]     96.875    18.750 0.96875 0.18750
[6,]    100.000     3.125 1.00000 0.03125
attr(,"target")
[1] 2.5
> sapply(crit,c)
    [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13] [,14]
low    0    1    1    1    2    2    2    3    3     3     4     4     5     5
up     6    6    7    8    8    9   10   10   11    12    12    13    13    14
    [,15] [,16] [,17] [,18] [,19] [,20] [,21]
low     5     6     6     6     7     7     8
up     15    15    16    17    17    18    18
> # 5:1 odds
> asymmetric.crit <- critVal.alpha(5:25,c(1,5)/6,alpha=0.05,
+                       matrix(1,nr=50,nc=21))
> # show the critical regions
> par(mfrow=c(1,2))
> gRxPlot(crit,method="critical")
> gRxPlot(asymmetric.crit,method="critical")
> rm(crit,asymmetric.crit)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>