This function returns a brief summary of the comparison between two (expanded) profiles.

Description

Function to return a brief summary of the comparison between two (expanded) profiles.

Usage

compSummary(l, decs = 6)

Arguments

Value

A data frame with the summarized results of each comparison. The values contained are: Sqr.Eucl.Dist: The squared euclidean distance, Standard Err: The standard error estimate, pValue p value of the test, low conf.intLower value for the desired confidence interval, up conf.intUpper value for the desired condfidence interval.

Author(s)

Alex Sanchez

Examples

# (NOT RUN)
# data(prostateIds)
# expandedWelsh <- expandedProfile(welsh01EntrezIDs[1:100], onto="MF",
#                        level=2, orgPackage="org.Hs.eg.db")
# expandedSingh <- expandedProfile(singh01EntrezIDs[1:100], onto="MF",
#                        level=2, orgPackage="org.Hs.eg.db")
# commonGenes <- intersect(welsh01EntrezIDs[1:100], singh01EntrezIDs[1:100])
# commonExpanded <- expandedProfile(commonGenes, onto="MF", level=2, orgPackage="org.Hs.eg.db")
# comparedMF <-compareGOProfiles (pn=expandedWelsh, 
#                           qm  = expandedSingh, 
#                           pqn0= commonExpanded)
# print(comparedMF)
# print(compSummary(comparedMF))
#

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(goProfiles)
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")'.

Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: GO.db

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/goProfiles/compSummary.Rd_%03d_medium.png", width=480, height=480)
> ### Name: compSummary
> ### Title: This function returns a brief summary of the comparison between
> ###   two (expanded) profiles.
> ### Aliases: compSummary
> ### Keywords: htest
> 
> ### ** Examples
> 
> # (NOT RUN)
> # data(prostateIds)
> # expandedWelsh <- expandedProfile(welsh01EntrezIDs[1:100], onto="MF",
> #                        level=2, orgPackage="org.Hs.eg.db")
> # expandedSingh <- expandedProfile(singh01EntrezIDs[1:100], onto="MF",
> #                        level=2, orgPackage="org.Hs.eg.db")
> # commonGenes <- intersect(welsh01EntrezIDs[1:100], singh01EntrezIDs[1:100])
> # commonExpanded <- expandedProfile(commonGenes, onto="MF", level=2, orgPackage="org.Hs.eg.db")
> # comparedMF <-compareGOProfiles (pn=expandedWelsh, 
> #                           qm  = expandedSingh, 
> #                           pqn0= commonExpanded)
> # print(comparedMF)
> # print(compSummary(comparedMF))
> #
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>