# Network Analysis of Immune Repertoire

## Documentation for package ‘NAIR’ version 1.0.4

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

NAIR-package | NAIR: Network Analysis of Immune Repertoire
addClusterLabels | Label Clusters in a Network Graph Plot
addClusterMembership | Partition a Network Graph Into Clusters
addClusterStats | Compute Cluster-Level Network Properties
addGraphLabels | Label Nodes in a Network Graph Plot
addNodeNetworkStats | Compute Node-Level Network Properties
addNodeStats | Compute Node-Level Network Properties
addPlots | Generate Plots of a Network Graph
aggregateIdenticalClones | Aggregate Counts/Frequencies for Clones With Identical Receptor Sequences
buildAssociatedClusterNetwork | Build Global Network of Associated TCR/BCR Clusters
buildNet | Network Analysis of Immune Repertoire
buildPublicClusterNetwork | Build Global Network of Public TCR/BCR Clusters
buildPublicClusterNetworkByRepresentative | Build Global Network of Public TCR/BCR Clusters Using Representative Clones
buildRepSeqNetwork | Network Analysis of Immune Repertoire
chooseNodeStats | Specify Node-level Network Properties to Compute
combineSamples | Load and Combine Data From Multiple Samples
exclusiveNodeStats | Specify Node-level Network Properties to Compute
extractLayout | Get Coordinate Layout From Graph Plot
filterInputData | Filter Data Rows and Subset Data Columns
findAssociatedClones | Identify TCR/BCR Clones in a Neighborhood Around Each Associated Sequence
findAssociatedSeqs | Identify TCR/BCR Sequences Associated With a Binary Variable
findAssociatedSeqs2 | Identify TCR/BCR Sequences Associated With a Binary Variable
findPublicClusters | Find Public Clusters Among RepSeq Samples
generateAdjacencyMatrix | Compute Graph Adjacency Matrix for Immune Repertoire Network
generateNetworkFromAdjacencyMat | Generate the 'igraph' for a Network Adjacency Matrix
generateNetworkGraph | Generate the 'igraph' for a Network Adjacency Matrix
generateNetworkGraphPlots | Generate Plots of a Network Graph
generateNetworkObjects | Generate Basic Output for an Immune Repertoire Network
getClusterStats | Compute Cluster-Level Network Properties
getNeighborhood | Identify Cells or Clones in a Neighborhood Around a Target Sequence
hamDistBounded | Bounded Computation of Hamming Distance
labelClusters | Label Clusters in a Network Graph Plot
labelNodes | Label Nodes in a Network Graph Plot
levDistBounded | Bounded Computation of Levenshtein Distance
loadDataFromFileList | Load and Combine Data From Multiple Samples
NAIR | NAIR: Network Analysis of Immune Repertoire
node_stat_settings | Specify Node-level Network Properties to Compute
plotNetworkGraph | Plot the Graph of an Immune Repertoire Network
saveNetwork | Save List of Network Objects
saveNetworkPlots | Write Plots to a PDF
simulateToyData | Generate Toy AIRR-Seq Data
sparseAdjacencyMatFromSeqs | Compute Graph Adjacency Matrix for Immune Repertoire Network