ngenes: Returns the number of genes that lead to this GO profile (an...

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

Description

The information contained in one or more lists of genes may be summarized by their GO profiles, that is to say, the absolute or relative frequencies of annotations or hits in all the classes or nodes of a given leven in a given GO ontology, or by the corresponding frequencies in a selected set of nodes (possibly belonging to more than one GO level but not hierarchicaly related). This function returns the number of genes in each list that were annotated to compute the profiles

Usage

ngenes(pn, i=NULL)
## Default S3 method:
ngenes(pn, i=NULL)
## S3 method for class 'numeric'
ngenes(pn, i=NULL)
## S3 method for class 'matrix'
ngenes(pn, i=NULL)
## S3 method for class 'ExpandedGOProfile'
ngenes(pn, i=NULL)
## S3 method for class 'BasicGOProfile'
ngenes(pn, i=NULL)

Arguments

pn	an object of class ExpandedGOProfile or BasicGOProfile representing one or more "sample" expanded GO profiles for a fixed ontology, or a numeric vector interpretable as a GO profile (expanded or not), or a frequency matrix (see the 'Details' section)
i	i-th profile in the case of more than one profiles. A vector with the number of genes of all profiles is returned if this argument is absent

Details

Given a list of n genes, and a set of s GO nodes X, Y, Z, ... in a given ontology (BP, MF or CC), its associated (contracted) "basic profile" is the frequencies vector (either absolute or relative frequencies) of annotations or hits of the n genes in each node. For a given node, say X, this frequency includes all annotations for X alone, for X and Y, for X and Z and so on. Thus, as relative frequencies, its sum is not necessarily one, or as absolute frequencies their sum is not necessarily n. On the other hand, an "expanded profile" corresponds to the frequencies in ALL OBSERVED NODE COMBINATIONS. That is, if n genes have been profiled, the expanded profile stands for the frequency of all hits EXCLUSIVELY in nodes X, Y, Z, ..., jointly with all hits simultaneously in nodes X and Y (and only in X and Y), simultaneously in X and Z, in Y and Z, ... , in X and Y and Z (and only in X,Y,Z), and so on. Thus, their sum is one.

An object of S3 class 'ExpandedGOProfile' is, essentially, a 'data.frame' object with each column representing an expanded profile. 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.

Value

A vector with the number of genes annotated in one or more GO profiles

Author(s)

Jordi Ocana

See Also

BasicGOProfile object, ExpandedGOProfile object

Examples

require("org.Hs.eg.db")
data(prostateIds) 
# To improve speed, use only the first 100 genes:
list1 <- welsh01EntrezIDs[1:100]
prof1 <- expandedProfile(list1, onto="MF", level=2, orgPackage="org.Hs.eg.db", na.rm=TRUE)$MF
length(list1)
# Only a subset of the initial gene list are annotated in the profile
ngenes(prof1)

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