Network Analysis of Immune Repertoire

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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