All functions

aggregateTaxa()

Aggregate a taxon abundance matrix

assignColorsToGroups()

Assign colors to groups

assignMetadataTypes()

Assign data types to metadata

barebonesCoNet()

Barebones R implementation of CoNet

buildNetwork()

Build a microbial network

clr()

Centered log-ratio (CLR) transform

compareDistribs()

Compare the distribution of a taxon across two groups

compareGroups()

Compare diversity-related properties across groups

exportToCoNet()

Export taxon abundances in a format suitable for CoNet

filterMetadata()

Filter metadata

filterTaxonMatrix()

Filter taxa in an abundance matrix

findClusters()

Cluster taxon- or sample-wise

floresgut_lineages

Lineages for gut taxa from Flores et al.

floresgut_metadata

Gut sample metadata from Flores et al.

floresgut_taxa

Gut taxon abundances from Flores et al.

getCoreTaxa()

List core taxa across groups

groupBarplot()

Bar plot of taxon composition with group support

ibd_functions

Functions from the PRISM cohort

ibd_lineages

Lineages for taxa from the PRISM cohort

ibd_metadata

Metadata for the PRISM cohort

ibd_taxa

IBD and control taxon abundances from the PRISM cohort

intersectTables()

Table intersection

makeColorsGivenMetadata()

Assign colors such that they encode a metadata item

mergeATC()

Merge ATC codes

mergeTables()

Table union

metadataToNumeric()

Convert metadata into numeric form

networkIntersectSig()

Significance of network intersection

normalize()

Normalize a matrix

removeGroupsWithMissingValues()

Remove groups that have metadata items with missing values

selectGroups()

Select groups

selectSamplesGivenMetadata()

Split samples into groups given metadata.

seqPCoA()

PCoA for microbial sequencing data

seqgroup

Analysis of Sequencing Data with Groups

setNAToGroupMean()

Replace missing values by group mean.

silhouette()

Get silhouette score for a clustering result

sortSamples()

Sort samples by group and optionally by time.

toPhyloseq()

Convert abundances to phyloseq object

transitionProbabs()

Compute transition probabilities between clusters