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Last data update: 2014.03.03

R: Compares two lists of genes by building (expanded) profiles...

compareGeneLists

R Documentation

Compares two lists of genes by building (expanded) profiles and comparing them

Description

This function wraps all the needed steps to compare two lists of genes following the methodology developed by Sanchez, Salicru and Ocan~a (2007)

Usage

compareGeneLists(genelist1, genelist2, idType = "Entrez", onto = "ANY",
level = 2, orgPackage, 
method = "lcombChisq", ab.approx = "asymptotic", confidence = 0.95, compareFunction="compareGOProfiles", ...)

Arguments

`genelist1`	First gene set to be compared
`genelist2`	Second gene set to be compared
`idType`	Type of identifiers for the genes. May be 'Entrez' (default), BiocProbes or GoTermsFrame. See the 'Details' section below
`onto`	Ontology on which the profile has to be built
`level`	Level of the ontology at which the profile has to be built
`orgPackage`	Name of a Bioconductor's organism annotations package ('org.Xx-eg-db')
`method`	The approximation method to the sampling distribution under the null hypothesis specifying that the samples pn and qm come from the same population. See the 'Details' section below
`confidence`	The confidence level of the confidence interval in the result
`ab.approx`	The approximation used for computing 'a' and 'b' coefficients (see details)
`compareFunction`	Allows to use 'fitGOProfile' (sample vs population) or 'compareGOProfiles' (sample1 vs sample2)
`...`	Other arguments for the methods 'basicProfile' or 'compareGoProfiles'

Value

The result of the comparison is a list with a variable number of arguments, depending for which ontologies has been performed the comparison. Each list member is an object of class 'htest' corresponding to the output of the function compareGOProfiles

Author(s)

Alex Sanchez

References

Sanchez-Pla, A., Salicru, M. and Ocana, J. Statistical methods for the analysis of high-throughput data based on functional profiles derived from the gene ontology. Journal of Statistical Planning and Inference, 2007

Examples

data(prostateIds)
prostateCompared<- compareGeneLists (welsh01EntrezIDs[1:500],
singh01EntrezIDs[1:500], level=2, onto='MF', orgPackage="org.Hs.eg.db")
print(prostateCompared)
# print(compSummary(prostateCompared))

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)

R is free software and comes with ABSOLUTELY NO WARRANTY.
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Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
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(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/compareGeneLists.Rd_%03d_medium.png", width=480, height=480)
> ### Name: compareGeneLists
> ### Title: Compares two lists of genes by building (expanded) profiles and
> ###   comparing them
> ### Aliases: compareGeneLists
> ### Keywords: htest
> 
> ### ** Examples
> 
> data(prostateIds)
> prostateCompared<- compareGeneLists (welsh01EntrezIDs[1:500],
+ singh01EntrezIDs[1:500], level=2, onto='MF', orgPackage="org.Hs.eg.db")

> print(prostateCompared)
$MF

	linear combination of chi-squares statistic

data:  expanded1[[i]] and expanded2[[i]] and common.expanded[[i]]
(n*m/(n+m)) * d2 = 1.5051, number of classes = 1.5000e+01, coef1 =
1.7731e-01, coef2 = 8.6333e-02, coef3 = 7.3047e-02, coef4 = 6.5930e-02,
coef5 = 4.8286e-02, coef6 = 4.1573e-02, coef7 = 3.9597e-02, coef8 =
1.7506e-02, coef9 = 1.6088e-02, coef10 = 9.9784e-03, coef11 =
3.4629e-03, coef12 = 3.4197e-03, coef13 = 3.4024e-03, coef14 =
2.4721e-03, coef15 = 8.6843e-04, coef16 = 1.2943e-04, coef17 =
6.3017e-05, coef18 = 5.3319e-05, coef19 = 4.8124e-05, coef20 =
3.5245e-05, coef21 = 3.0345e-05, coef22 = 2.8903e-05, coef23 =
1.2778e-05, coef24 = 1.1743e-05, coef25 = 7.2835e-06, coef26 =
2.5276e-06, coef27 = 2.4961e-06, coef28 = 2.4835e-06, coef29 =
1.8045e-06, coef30 = 6.3389e-07, p-value = 0.0206
alternative hypothesis: true squared Euclidean distance between the contracted profiles is greater than zero
95 percent confidence interval:
 0.0003515754 0.0122301701
sample estimates:
sample squared Euclidean distance 
                      0.006290873 
attr(,"se")
distance standard error 
            0.003030309 


> # print(compSummary(prostateCompared))
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>