Build a sparse adjacency matrix from TCRdist() results
TCRdist_to_sparse_matrix.Rd![[Experimental]](figures/lifecycle-experimental.svg)
Builds a sparse adjacency matrix from the edges_df/nodes_df
produced by TCRdist() (or cluster_tcrs() using sparseMatrix().
Arguments
- edges_df
a data frame with columns "node1_idx" and "node2_idx", such as
TCRdist()'s$edges_df.- nodes_df
a data frame with one row per node, such as
TCRdist()'s$nodes_df.- binary
if TRUE, the nonzero values in the matrix will all be 1, otherwise they will be equal to TCRdist between the two TCRs (default if FALSE).
Value
an n x n symmetric sparse matrix (class dsCMatrix), where
n = nrow(nodes_df). Entry [i, j] is 1 if the two TCRs are connected by an
edge (TCRdist <= cutoff) and 0 otherwise. Row/column names are nodes_df$tcr_index.
See also
TCRdist(), cluster_tcrs(), TCRdist_to_igraph()
Other tcr_similarity:
TCRdist(),
TCRdist_cpp(),
TCRdist_old(),
TCRdist_to_igraph(),
add_to_tcr_network(),
cluster_tcrs(),
plot_clusters()
Examples
load_example_data(dataset = "SJTRC_minimal")
#> Example data already loaded into object: 'SJTRC_minimal'
df = get_all_tcrs(SJTRC_minimal, chain="paired", remove_duplicates = TRUE)
result = TCRdist(df, tcrdist_cutoff = 90)
#> Removed 384 TCRs with unknown V-segments (1.2%) from a total of 32,164 TCRs.
#> Removed 10 TCRs with short CDR3 segments (0.031%) from a total of 31,780 TCRs.
#> Removed 13,326 TCRs with non-functional CDR3 amino acid sequences (42%) from a total of 31,770 TCRs.
#> Filtered data frame contains 18,444 TCRs (57%) of original 32,164 TCRs.
#> ℹ Number of chunks: 190
#> ℹ 10% done — time taken so far: 0.26 seconds
#> ℹ 20% done — time taken so far: 0.36 seconds
#> ℹ 30% done — time taken so far: 0.45 seconds
#> ℹ 40% done — time taken so far: 0.7 seconds
#> ℹ 50% done — time taken so far: 0.79 seconds
#> ℹ 60% done — time taken so far: 1.04 seconds
#> ℹ 70% done — time taken so far: 1.14 seconds
#> ℹ 80% done — time taken so far: 1.39 seconds
#> ℹ 90% done — time taken so far: 1.49 seconds
#> ℹ 100% done — time taken so far: 1.53 seconds
#> ✔ Total time taken: 1.53 seconds
adj_mat = TCRdist_to_sparse_matrix(result$edges_df, result$nodes_df)