compare_sequences: Compare Sequences Between Groups

In tna: Transition Network Analysis (TNA)

Compare Sequences Between Groups

Description

Performs comprehensive sequence comparison analysis between groups. All patterns of the sequences (subsequences of specific length) are extracted from all sequences in each group. For two groups, the proportions of the patterns between the groups are compared with a z-test for proportions. For more than two groups, the Chi-squared test is applied. Both tests are applied within patterns of the same length.

Usage

compare_sequences(x, ...)

## Default S3 method:
compare_sequences(x, group, sub, min_freq = 5L, correction = "bonferroni", ...)

## S3 method for class 'group_tna'
compare_sequences(x, sub, min_freq = 5L, correction = "bonferroni", ...)

Arguments

x	A group_tna object or a data.frame containing sequence data in wide format.
...	Not used.
group	A vector indicating the group assignment of each row of the data/sequence. Must have the same length as the number of rows/sequences of x. Alternatively, a single character string giving the column name of the data that defines the group when x is a wide format data.frame or a tna_data object.
sub	An integer vector of subsequence lengths to analyze. The default is 2:5.
min_freq	An integer giving the minimum number of times that a specific pattern has to be observed to be included in the analysis. The default is 5.
correction	A character string naming the multiple comparison correction method (default: "bonferroni"). Supports all stats::p.adjust methods: "holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none".

Value

A tna_sequence_comparison object, which is a data.frame with columns giving the names of the pattern, pattern frequencies, pattern proportions (within patterns of the same length), test statistic values and p-values of the tests.

See Also

Model comparison functions compare(), compare.group_tna(), plot.tna_comparison(), plot.tna_sequence_comparison(), plot_compare(), plot_compare.group_tna(), print.tna_comparison(), print.tna_sequence_comparison()

Examples

group <- c(rep("High", 1000), rep("Low", 1000))
comp <- compare_sequences(group_regulation, group)

tna documentation built on Nov. 5, 2025, 7:14 p.m.