Last data update: 2014.03.03

R: Check motif
testMotifR Documentation

Check motif

Description

This function adds random false positive edges to the regulatory prior and will check if they become pruned.

Usage

testMotif(x, motif, expr, ppi, mode = c("augment", "remove"), prop = 0.05,
  seed = 1, ...)

Arguments

x

Model regulatory network.

motif

Motif used to construct the model regulatory network.

expr

Expression matrix used to construct model network.

ppi

PPI used to construct model regulatory network.

mode

a character string - either "augment" to add random edges or "remove" to remove random edges.

prop

numeric specifying number of edges to augment or remove from regulatory prior, as a proportion of the number of edges in the regulatory prior.

seed

Random seed.

...

Options for the panda function.

Value

ggplot heatmap list of indices of net corresponding to each TF

Examples

data(pandaToyData)
data(pandaResult)
regnet = slot(pandaResult,"regNet")
with(pandaToyData, testMotif(regnet, motif, mode="augment", expression, ppi, hamming=1))

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 '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(pandaR)
Loading required package: Biobase
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

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/pandaR/testMotif.Rd_%03d_medium.png", width=480, height=480)
> ### Name: testMotif
> ### Title: Check motif
> ### Aliases: testMotif
> 
> ### ** Examples
> 
> data(pandaToyData)
> data(pandaResult)
> regnet = slot(pandaResult,"regNet")
> with(pandaToyData, testMotif(regnet, motif, mode="augment", expression, ppi, hamming=1))
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>