Package index • NAIR

Main Function

buildRepSeqNetwork() buildNet(): Network Analysis of Immune Repertoire

Searching for Associated TCR/BCR Clusters

Given multiple samples of AIRR-Seq data, search for TCR/BCR clusters associated with a binary variable of interest

findAssociatedSeqs() findAssociatedSeqs2(): Identify TCR/BCR Sequences Associated With a Binary Variable

findAssociatedClones(): Identify TCR/BCR Clones in a Neighborhood Around Each Associated Sequence

buildAssociatedClusterNetwork(): Build Global Network of Associated TCR/BCR Clusters

Searching for Public TCR/BCR Clusters

Search for public TCR/BCR clusters across multiple samples of AIRR-seq data

findPublicClusters(): Find Public Clusters Among RepSeq Samples

buildPublicClusterNetwork(): Build Global Network of Public TCR/BCR Clusters

buildPublicClusterNetworkByRepresentative(): Build Global Network of Public TCR/BCR Clusters Using Representative Clones

Network Properties

Compute network properties and perform cluster analysis

addNodeStats(): Compute Node-Level Network Properties

chooseNodeStats() exclusiveNodeStats(): Specify Node-level Network Properties to Compute

addClusterMembership(): Partition a Network Graph Into Clusters

addClusterStats(): Compute Cluster-Level Network Properties

getClusterStats(): Compute Cluster-Level Network Properties

Network Visualization

Generate or modify plots of a network graph

addPlots() generateNetworkGraphPlots(): Generate Plots of a Network Graph

labelClusters() addClusterLabels(): Label Clusters in a Network Graph Plot

labelNodes() addGraphLabels(): Label Nodes in a Network Graph Plot

extractLayout(): Get Coordinate Layout From Graph Plot

Manual Generation of Network Components

generateNetworkObjects(): Generate Basic Output for an Immune Repertoire Network

generateNetworkGraph() generateNetworkFromAdjacencyMat(): Generate the igraph for a Network Adjacency Matrix

generateAdjacencyMatrix() sparseAdjacencyMatFromSeqs(): Compute Graph Adjacency Matrix for Immune Repertoire Network

Loading, Filtering and Saving Data

loadDataFromFileList() combineSamples(): Load and Combine Data From Multiple Samples

filterInputData(): Filter Data Rows and Subset Data Columns

aggregateIdenticalClones(): Aggregate Counts/Frequencies for Clones With Identical Receptor Sequences

getNeighborhood(): Identify Cells or Clones in a Neighborhood Around a Target Sequence

saveNetwork(): Save List of Network Objects

saveNetworkPlots(): Write Plots to a PDF

Distance Functions

Used to quantify similarity between receptor sequences

hamDistBounded(): Bounded Computation of Hamming Distance

levDistBounded(): Bounded Computation of Levenshtein Distance

Other Functions and Topics

simulateToyData(): Generate Toy AIRR-Seq Data

NAIR NAIR-package: NAIR: Network Analysis of Immune Repertoire

Deprecated Functions

addNodeNetworkStats() deprecated: Compute Node-Level Network Properties

plotNetworkGraph() deprecated: Plot the Graph of an Immune Repertoire Network