compare_sequence_subsequences: Compare subsequence prevalence between groups

In gp3sequences: Transparent Analysis of Ordered Categorical Sequences

Compare subsequence prevalence between groups

Description

Performs transparent contingency-table tests on sequence-level presence. Multiple testing is adjusted explicitly. Results are associational unless a randomized design independently justifies causal interpretation.

Usage

compare_sequence_subsequences(
  occurrences,
  group_col,
  test = c("auto", "chisq", "fisher"),
  p_adjust = "BH",
  min_sequence_count = 1L
)

Arguments

occurrences	A non-contiguous subsequence occurrence table.
group_col	Sequence-constant group column retained through metadata_cols during extraction.
test	"auto", "chisq", or "fisher".
p_adjust	Multiple-testing adjustment method.
min_sequence_count	Minimum total sequence count per subsequence.

Value

A data frame of prevalence contrasts and adjusted p-values.

Examples

data <- data.frame(
  sequence_id = rep(paste0("s", 1:4), each = 4L),
  sequence_order = rep(1:4, 4L),
  state = c("A", "B", "C", "D", "A", "B", "D", "D",
            "D", "C", "B", "A", "D", "C", "A", "A"),
  group = rep(c("g1", "g2"), each = 8L)
)
occurrences <- extract_sequence_subsequences(data, metadata_cols = "group")
compare_sequence_subsequences(occurrences, "group")

gp3sequences documentation built on Aug. 23, 2026, 5:10 p.m.