equivalentGOProfiles: Are two lists of genes equivalent in terms of their Gene...

In alexsanchezpla/goProfiles: goProfiles: an R package for the statistical analysis of functional profiles

Description

Performs an equivalence test based on the squared Euclidean distance between the Gene Ontology profiles of two lists of genes. Equivalence is declared if the upper limit d.sup of a one-sided confidence interval [0, d.sup] for the distance is lesser than the equivalence limit d0.

Usage

equivalentGOProfiles(goObject, ...)
## S3 method for class 'GOProfileHtest'
equivalentGOProfiles(goObject, equivEpsilon = 0.05, d0 = NULL, confidence = NULL, ...)
## S3 method for class 'ExpandedGOProfile'
equivalentGOProfiles(goObject, qm=NULL, pqn0=NULL,
    n = ngenes(goObject), m = ngenes(qm), n0 = ngenes(pqn0),
    confidence = 0.95,
    equivEpsilon = 0.05, d0 = NULL,
    simplify = FALSE, ...)
## Default S3 method:
equivalentGOProfiles(goObject, ...)

Arguments

goObject	an object related to GO profiles or comparisons between them
qm	an expanded GO profile, i.e. and object of class 'ExpandedGOProfile'
pqn0	an expanded GO profile, i.e. and object of class 'ExpandedGOProfile'
n	a numeric vector with the number of genes profiled in each column of goObject. This parameter is included to allow the possibility of exploring the consequences of varying sample sizes, other than the true sample size in goObject.
m	a numeric vector with the number of genes profiled in each column of qm.
n0	a numeric vector with the number of genes profiled in each column of pqn0.
confidence	the nominal confidence level of the one-sided confidence interval on the distance
d0	a positive value specifying the equivalence limit
equivEpsilon	a positive value used to compute 'd0' if it is not directly available
simplify	should the result be simplified, if possible? See the 'Details' section
...	further arguments, tipically the same than to 'compareGOProfiles'

Details

An object of S3 class "ExpandedGOProfile" is, essentially, a "data.frame" object with each column representing the relative frequencies in all observed node combinations, resulting from profiling a set of genes, for a given and fixed ontology. The 'row.names' attribute codifies the node combinations and each "data.frame" column (say, each profile) has an attribute, 'ngenes', indicating the number of profiled genes.

In the 'ExpandedGOProfile' interface, the arguments 'goObject', 'qm' and 'pqn0' are compared in a column by column wise, recycling columns, if necessary, in order to perform max(ncol(goObject),ncol(qm),ncol(pqn0)) equivalence tests (each test resulting in an object of class 'htest'). In order to be properly tested, these arguments are expanded by row, according to their row names. That is, the data arguments can have unequal row numbers. Then, they are expanded adding rows with zero frequencies, in order to make them comparable. In the i-th comparison (i from 1 to max(ncol(goObject),ncol(qm),ncol(pqn0))), the parameters n, m and n0 are included to allow the possibility of exploring the consequences of varying sample sizes, other than the true sample sizes included as an attribute in goObject, qm and pqn0. When qm = NULL, the genes profiled in goObject are compared with a subsample of them, those profiled in pqn0 (is there equivalence between a set of genes and a restricted subset, e.g. those overexpressed under a disease, in terms of their profiles?). When pqn0 = NULL, an equivalence test between two profiles with no genes in common is performed.

In the 'GOProfileHtest' interface, the one-sided confidence interval for the squared Euclidean distance is computed from the distance and its standard error stored in the corresponding fields of the argument goObject, itself typically an object of class 'GOProfileHtest' resulting from a call to 'compareGOProfiles' with simplify=T.

In the default interface, the 'goObject' argument is previously converted into an object of class 'ExpandedGOProfile' and then this interface is used.

If the argument 'd0' is not provided it is computed as d0 <- s * equivEpsilon^2, where 's' stands for the number of non empty GO nodes in any of the GO profiles being compared.

Value

In the 'ExpandedGOProfile' interface, the result is an object of class "list" containg one or more "htest" objects, each of which may come from previous profiles comparisons. In the other interfaces, the result is a single "htest" object. Each one of these "htest" objects has the following fields:

statistic	test statistic, (distance - d0) / se
parameter	d0 and the sample sizes (number of genes) n and m
p.value	associated p-value to test the null hypothesis of profiles inequivalence
conf.int	asymptotic one-sided confidence interval for the squared euclidean distance. Its attribute "conf.level" contains its nominal confidence level.
estimate	squared euclidean distance between the contracted profiles. Its attribute "se" contains its standard error estimate
data.name	a character string giving the names of the data
alternative	a character string describing the alternative hypothesis (always 'Equivalence or similarity, true squared Euclidean distance between the contracted profiles is less than d0'

Author(s)

Jordi Ocana

See Also

'compareGOProfiles'

Examples

data(prostateIds)

expandedWelsh <- expandedProfile(welsh01EntrezIDs[1:100], onto="ANY",
                                 level=2, orgPackage="org.Hs.eg.db")
expandedSingh <- expandedProfile(singh01EntrezIDs[1:100], onto="ANY",
                                 level=2, orgPackage="org.Hs.eg.db")
commonGenes <- intersect(welsh01EntrezIDs[1:100], singh01EntrezIDs[1:100])
commonExpanded <- expandedProfile(commonGenes, onto="ANY", level=2, 
                                  orgPackage="org.Hs.eg.db")

### FUnciona si fem: 

equivMF <-equivalentGOProfiles (expandedWelsh[["MF"]], 
                              qm  = expandedSingh[["MF"]], 
                              pqn0= commonExpanded[["MF"]])

equivsList <- lapply(1:length(expandedWelsh), 
                     function (onto){
                          equivalentGOProfiles (expandedWelsh[[onto]], 
                                qm  = expandedSingh[[onto]], 
                                pqn0= commonExpanded[[onto]])
                     }
)

alexsanchezpla/goProfiles documentation built on May 28, 2019, 4:54 p.m.