buildAssociatedClusterNetwork: Build Global Network of Associated TCR/BCR Clusters

In mlizhangx/Network-Analysis-for-Repertoire-Sequencing-: Network Analysis of Immune Repertoire

Build Global Network of Associated TCR/BCR Clusters

Description

Part of the workflow Searching for Associated TCR/BCR Clusters. Intended for use following findAssociatedClones().

Given data containing a neighborhood of similar clones around each associated sequence, combines the data into a global network and performs network analysis and cluster analysis.

Usage

buildAssociatedClusterNetwork(
  file_list,
  input_type = "rds",
  data_symbols = "data", header = TRUE, sep,
  read.args = list(row.names = 1),
  seq_col,
  min_seq_length = NULL,
  drop_matches = NULL,
  drop_isolated_nodes = FALSE,
  node_stats = TRUE,
  stats_to_include =
    chooseNodeStats(cluster_id = TRUE),
  cluster_stats = TRUE,
  color_nodes_by = "GroupID",
  output_name = "AssociatedClusterNetwork",
  verbose = FALSE,
  ...
)

Arguments

file_list	A character vector of file paths, or a list containing connections and file paths. Each element corresponds to a single file containing the data for a single sample. Passed to loadDataFromFileList().
input_type	A character string specifying the file format of the neighborhood data files. Options are "table", "txt", "tsv", "csv", "rds" and "rda". Passed to loadDataFromFileList().
data_symbols	Used when input_type = "rda". Specifies the name of each neighborhood's data frame within its respective Rdata file. Passed to loadDataFromFileList().
header	For values of input_type other than "rds" and "rda", this argument is used to specify the value of the header argument to read.table(), read.csv(), etc.
sep	For values of input_type other than "rds" and "rda", this argument can be used to specify a non-default value of the sep argument to read.table(), read.csv(), etc.
read.args	For values of input_type other than "rds" and "rda", this argument is used to specify values of optional arguments to read.table(), read.csv(), etc. Accepts a named list of argument values. Values of header and sep in this list take precedence over values specified via the header and sep arguments.
seq_col	Specifies the column of each neighborhood's data frame containing the TCR/BCR sequences. Accepts a character string containing the column name or a numeric scalar containing the column index.
min_seq_length	Passed to buildRepSeqNetwork() when constructing the global network.
drop_matches	Passed to buildRepSeqNetwork() when constructing the global network.
drop_isolated_nodes	Passed to buildRepSeqNetwork() when constructing the global network.
node_stats	Passed to buildRepSeqNetwork() when constructing the global network.
stats_to_include	Passed to buildRepSeqNetwork() when constructing the global network.
cluster_stats	Passed to buildRepSeqNetwork() when constructing the global network.
color_nodes_by	Passed to buildRepSeqNetwork() when constructing the global network.
output_name	Passed to buildRepSeqNetwork() when constructing the global network.
verbose	Logical. If TRUE, generates messages about the tasks performed and their progress, as well as relevant properties of intermediate outputs. Messages are sent to stderr().
...	Other arguments to buildRepSeqNetwork() when constructing the global network.

Details

Each associated sequence's neighborhood contains clones (from all samples) with TCR/BCR sequences similar to the associated sequence. The neighborhoods are assumed to have been previously identified using findAssociatedClones().

The neighborhood data for all associated sequences are used to construct a single global network. Cluster analysis is used to partition the global network into clusters, which are considered as the associated TCR/BCR clusters. Network properties for the nodes and clusters are computed and returned as metadata. A plot of the global network graph is produced, with the nodes colored according to the binary variable of interest.

See the Searching for Associated TCR/BCR Clusters article on the package website for more details.

Value

A list of network objects as returned by buildRepSeqNetwork(). The list is returned invisibly. If the input data contains a combined total of fewer than two rows, or if the global network contains no nodes, then the function returns NULL, invisibly, with a warning.

Author(s)

Brian Neal ([e-mail])

References

Hai Yang, Jason Cham, Brian Neal, Zenghua Fan, Tao He and Li Zhang. (2023). NAIR: Network Analysis of Immune Repertoire. Frontiers in Immunology, vol. 14. doi: 10.3389/fimmu.2023.1181825

Webpage for the NAIR package

Searching for Associated TCR/BCR Clusters article on package website

See Also

findAssociatedSeqs() findAssociatedClones()

Examples

set.seed(42)

## Simulate 30 samples from two groups (treatment/control) ##
n_control <- n_treatment <- 15
n_samples <- n_control + n_treatment
sample_size <- 30 # (seqs per sample)
base_seqs <- # first five are associated with treatment
  c("CASSGAYEQYF", "CSVDLGKGNNEQFF", "CASSIEGQLSTDTQYF",
    "CASSEEGQLSTDTQYF", "CASSPEGQLSTDTQYF",
    "RASSLAGNTEAFF", "CASSHRGTDTQYF", "CASDAGVFQPQHF")
# Relative generation probabilities by control/treatment group
pgen_c <- matrix(rep(c(rep(1, 5), rep(30, 3)), times = n_control),
                 nrow = n_control, byrow = TRUE)
pgen_t <- matrix(rep(c(1, 1, rep(1/3, 3), rep(2, 3)), times = n_treatment),
                 nrow = n_treatment, byrow = TRUE)
pgen <- rbind(pgen_c, pgen_t)
simulateToyData(
  samples = n_samples,
  sample_size = sample_size,
  prefix_length = 1,
  prefix_chars = c("", ""),
  prefix_probs = cbind(rep(1, n_samples), rep(0, n_samples)),
  affixes = base_seqs,
  affix_probs = pgen,
  num_edits = 0,
  output_dir = tempdir(),
  no_return = TRUE
)

## Step 1: Find Associated Sequences ##
sample_files <-
  file.path(tempdir(),
            paste0("Sample", 1:n_samples, ".rds")
  )
group_labels <- c(rep("reference", n_control),
                  rep("comparison", n_treatment))
associated_seqs <-
  findAssociatedSeqs(
    file_list = sample_files,
    input_type = "rds",
    group_ids = group_labels,
    seq_col = "CloneSeq",
    min_seq_length = NULL,
    drop_matches = NULL,
    min_sample_membership = 0,
    pval_cutoff = 0.1
  )
head(associated_seqs[, 1:5])

## Step 2: Find Associated Clones ##
dir_step2 <- tempfile()
findAssociatedClones(
  file_list = sample_files,
  input_type = "rds",
  group_ids = group_labels,
  seq_col = "CloneSeq",
  assoc_seqs = associated_seqs$ReceptorSeq,
  min_seq_length = NULL,
  drop_matches = NULL,
  output_dir = dir_step2
)

## Step 3: Global Network of Associated Clusters ##
associated_clusters <-
  buildAssociatedClusterNetwork(
    file_list = list.files(dir_step2,
                           full.names = TRUE
    ),
    seq_col = "CloneSeq",
    size_nodes_by = 1.5,
    print_plots = TRUE
  )

mlizhangx/Network-Analysis-for-Repertoire-Sequencing- documentation built on April 7, 2024, 12:02 p.m.