Compute alpha weights

Description

Transform a vector of p-values into weights.

Usage

alphaMLG(pv, threshold = max(pv))

Arguments

Details

Computes a set of weights from p-values using the formula -log10(pv/threshold).

Author(s)

Calin Voichita and Sorin Draghici

See Also

pe

Examples

load(system.file("extdata/E-GEOD-21942.topTable.RData", package = "ROntoTools"))

head(alphaMLG(top$adj.P.Val))

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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> library(ROntoTools)
Loading required package: graph
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: boot
Loading required package: KEGGREST
Loading required package: KEGGgraph

Attaching package: 'KEGGgraph'

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

    plot

Loading required package: Rgraphviz
Loading required package: grid
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/ROntoTools/alphaMLG.Rd_%03d_medium.png", width=480, height=480)
> ### Name: alphaMLG
> ### Title: Compute alpha weights
> ### Aliases: alphaMLG
> 
> ### ** Examples
> 
> 
> load(system.file("extdata/E-GEOD-21942.topTable.RData", package = "ROntoTools"))
> 
> head(alphaMLG(top$adj.P.Val))
[1] 8.379024 8.379024 8.013694 7.753777 7.753777 7.595237
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>