OTU2Taxa-OTU2Taxa: OTU2Taxa

In lauzingaretti/LinkHD: LinkHD: a versatile framework to explore and integrate heterogeneous data

OTU2Taxa

Description

This function aggregates OTUs into their taxonomic characteristics,i.e. genera or family level and returns a 'Taxonomic Enrichment Test' by using the hypergeometric distribution function P(x>=X), which gives the probability of a particular genera/family has been selected by chance. This function determines whether a selected set of genera/family shows a statistically significant difference in comparison with the genera/family into the whole samples. This method is used to identify selected families or genus that are over-represented in a large set of OTUs. The output may have an important biological meaning since the selected genus/families can be associated with phenotypes. The function outputs -log(p+0.05), i.e. a higher value means an 'enriched' genus or family.

Usage

OTU2Taxa(Selection, TaxonInfo, tableName, AnalysisLev = "Genus")

Arguments

Selection	list or data frame from VarSelection or dAB function
TaxonInfo	data.frame with taxonomic table associated to Data input. For instance, if Data comes from 16_S level, TaxoInfo should be a data.frame with 16_S associated taxonomic information. Note that the first column of this table must have the OTUs ids.
tableName	a character indicating the table name. For instance, if your data comes from 16_S, this parameter should be '16_S'. Importantly, this argument should match with the names from the input list, ExpressionSet or MultiAssayExperiment object, which corresponds the Data argument of LinkData function.
AnalysisLev	It is a character indicating if data should be aggregate into genera or family level

Value

List. The function outputs a list of size two. The first element contains all the selected taxa with their associated value from the hyperg distribution -log(p+0.05); whereas the second element only includes taxas' counting up to 1.

Author(s)

Laura M Zingatetti

References

2. Da Wei Huang, B. T. S., & Lempicki, R. A. (2009). Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic acids research, 37(1), 1.

3. Zheng, Q., & Wang, X. J. (2008). GOEAST: a web-based software toolkit for Gene Ontology enrichment analysis. Nucleic acids research, 36(suppl_2), W358-W363.

Examples

{
data('Ruminotypes')
Normalization<-lapply(list(Ruminotypes$`16_S`,Ruminotypes$Archaea,Ruminotypes$`18_S`),
function(x){DataProcessing(x,Method='Compositional')})
Dataset<-Normalization
names(Dataset)<-c('16_S','Archaea','18_S')
#Running LinkData
Output<-LinkData(Dataset,Distance=rep('euclidean',3),
Scale = FALSE,Center=FALSE,nCluster = 3)
Select_Var<-VarSelection(Output,Data=Dataset,Crit = 'Rsquare',perc=0.9)
SignTaxa<-OTU2Taxa(Selection=VarTable(Select_Var),
TaxonInfo=Ruminotypes$Taxa_16S,tableName='16_S',AnalysisLev = 'Family')
Selected<-SignTaxa$TotalUp1
}

lauzingaretti/LinkHD documentation built on March 7, 2023, 9:21 a.m.