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aggregateTaxa()
|
Aggregate a taxon abundance matrix |
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assignColorsToGroups()
|
Assign colors to groups |
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assignMetadataTypes()
|
Assign data types to metadata |
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barebonesCoNet()
|
Barebones R implementation of CoNet |
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buildNetwork()
|
Build a microbial network |
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clr()
|
Centered log-ratio (CLR) transform |
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compareDistribs()
|
Compare the distribution of a taxon across two groups |
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compareGroups()
|
Compare diversity-related properties across groups |
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exportToCoNet()
|
Export taxon abundances in a format suitable for CoNet |
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filterMetadata()
|
Filter metadata |
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filterTaxonMatrix()
|
Filter taxa in an abundance matrix |
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findClusters()
|
Cluster taxon- or sample-wise |
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floresgut_lineages
|
Lineages for gut taxa from Flores et al. |
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floresgut_metadata
|
Gut sample metadata from Flores et al. |
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floresgut_taxa
|
Gut taxon abundances from Flores et al. |
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getCoreTaxa()
|
List core taxa across groups |
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groupBarplot()
|
Bar plot of taxon composition with group support |
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ibd_functions
|
Functions from the PRISM cohort |
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ibd_lineages
|
Lineages for taxa from the PRISM cohort |
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ibd_metadata
|
Metadata for the PRISM cohort |
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ibd_taxa
|
IBD and control taxon abundances from the PRISM cohort |
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intersectTables()
|
Table intersection |
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makeColorsGivenMetadata()
|
Assign colors such that they encode a metadata item |
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mergeATC()
|
Merge ATC codes |
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mergeTables()
|
Table union |
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metadataToNumeric()
|
Convert metadata into numeric form |
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networkIntersectSig()
|
Significance of network intersection |
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normalize()
|
Normalize a matrix |
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removeGroupsWithMissingValues()
|
Remove groups that have metadata items with missing values |
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selectGroups()
|
Select groups |
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selectSamplesGivenMetadata()
|
Split samples into groups given metadata. |
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seqPCoA()
|
PCoA for microbial sequencing data |
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seqgroup
|
Analysis of Sequencing Data with Groups |
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setNAToGroupMean()
|
Replace missing values by group mean. |
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silhouette()
|
Get silhouette score for a clustering result |
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sortSamples()
|
Sort samples by group and optionally by time. |
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toPhyloseq()
|
Convert abundances to phyloseq object |
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transitionProbabs()
|
Compute transition probabilities between clusters |