OTU2Taxa-OTU2Taxa: OTU2Taxa

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

Description

This function aggregates OTUs into their taxonomic characteristics (genus or level)and it analyses the most significant selected genera into each table. To each genera, the function returns the hypergeometric distribution function P(x>=X) to each count. The function also returns filtered data by counts higher than one. In both cases, we implemented -log(p+0.05), then a higher value means more significant, i.e., it is an enrichment 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'. Note that, this argument must mutch with the names from the input list into LinkData function.
AnalysisLev	It is a character indicating if data should be aggregate to genera or family level

Value

List. The first element of this list contains all the selected taxa with their associated value from the hyperg distribution -log(p+0.05); the second element of this list have only 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-examples documentation built on Dec. 21, 2021, 9:42 a.m.