README.md

In YushuShi/looPA: Microbiome Feature Identification Using Leave-One-Out with Permanova Assessment

looPA: Microbiome feature identification using leave-one-out with Permanova assessment

looPA is a permutation based method, which can account for phylogenetic relatedness between taxonomic features and identify important features for further investigation.

Usage

looPA(otutable,taxonomy, sampleInfo, outcomeVar, numRep=200,useMoreCores=TRUE,
      tree=NULL,distanceMetric="Bray Curtis")

Parameters

|Parameters || |------|-----| |otutable| OTU table. Rows correspond to OTUs while columns correspond to samples. Row names (OTU names) and column names(sample names) must be provided.| |taxonomy| Taxonomy table. Rows correspond to OTUs while columns correspond to the taxonomic levels. Row names (OTU names) must match the row names of the OTU table.| |sampleInfo| Patient information. Rows correspond to samples while columns correspond to covariates. Row names (sample names) must match the column names of the OTU table.| |outcomeVar| The outcome of interest. For now we only accept single covariate.| |numRep| Number of repeated PERMANOVA test for each feature. Default is 200.| |useMoreCores| Shall we use more cores of the computer for this job? By default, the number of cores used will be the number of cores of the computer -1. If you give an integer value, looPA will use it as the number of cores you want to use.| |tree| The phylogenetic information correspond to OTU table.| |distanceMetric| The distance metric used in PERMANOVA test. We offer three choices, "Bray Curtis" (the default), "Unweighted UniFrac"(requires tree information), and "Weighted UniFrac"(requires tree information).|

Results

|Results|| |------|-----| |looPAresult| A dataframe with the names of the selected taxa and their medians and confidence intervals over repeated PERMANOVA tests.| |looPAplot| A plot showing the selected features.|

Example

library(looPA)
outcomeVar<-"Response"

looPAResult<-looPA(otutable,taxonomy, sampleInfo, outcomeVar,useMoreCores=TRUE,
tree=tree,distanceMetric="Weighted UniFrac")

YushuShi/looPA documentation built on May 7, 2020, 9:38 p.m.