Package 'cellchatr'

Return string "Hello world!" to R.

Description

Return string "Hello world!" to R.

Usage

hello_world()

Value

A character string "Hello world!"

Examples

hello_world()

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Match overexpressed genes against CellChatDB ligand-receptor pairs.

Description

Match overexpressed genes against CellChatDB ligand-receptor pairs.

Usage

rust_match_lr_pairs(overexpressed, lr_ligands, lr_receptors, lr_names)

Arguments

overexpressed	Character vector of overexpressed gene names.
lr_ligands	Character vector of ligands from CellChatDB.
lr_receptors	Character vector of receptors from CellChatDB.
lr_names	Character vector of interaction names from CellChatDB.

Value

Character vector of matched interaction names.

Complexity

• Time: O(m + r) where m = overexpressed genes, r = LR pairs

• Space: O(m) for HashSet

• R equivalent (%%in%% twice): O(m x r)

Examples

rust_match_lr_pairs(
  c("TGFB1", "VEGFA"),
  c("TGFB1", "MYC", "VEGFA"),
  c("TGFBR1", "MYCBP", "FLT1"),
  c("TGFB1_TGFBR1", "MYC_MYCBP", "VEGFA_FLT1")
)

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Filter expression matrix genes to only those present in CellChatDB.

Description

Filter expression matrix genes to only those present in CellChatDB.

Usage

rust_subset_genes(expr_genes, db_genes)

Arguments

expr_genes	Character vector of gene names from expression matrix.
db_genes	Character vector of gene names from CellChatDB.

Value

Character vector of genes present in both inputs.

Complexity

• Time: O(n + m) where n = db_genes, m = expr_genes

• Space: O(n) for HashSet

• R equivalent (%%in%%): O(n x m)

Examples

rust_subset_genes(
  c("TGFB1", "VEGFA", "GAPDH"),
  c("TGFB1", "VEGFA", "MYC")
)

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Identify over-expressed genes per cell type using Wilcoxon rank-sum test.

Description

Identify over-expressed genes per cell type using Wilcoxon rank-sum test.

Usage

rust_wilcoxon_filter(counts, labels, gene_names, pval_threshold)

Arguments

counts	NumericMatrix of gene expression (genes x cells).
labels	Character vector of cell type labels, one per cell.
gene_names	Character vector of gene names.
pval_threshold	P-value cutoff for significance.

Value

Character vector of over-expressed gene names.

Complexity

• Time: O((g/p) x k x c log c) where g = genes, p = CPU cores, k = cell types, c = cells

• Space: O(c) per gene

• R equivalent: O(g x k x c log c) — serial, no parallelism

Examples

counts <- matrix(c(rep(10, 50), rep(0, 50), rep(1, 100)),
  nrow = 2, byrow = TRUE)
labels <- c(rep("A", 50), rep("B", 50))
rust_wilcoxon_filter(counts, labels, c("TGFB1", "GAPDH"), 0.05)

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