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_tnaobject or adata.framecontaining sequence data in wide format.- ...
Not used.
- group
A
vectorindicating the group assignment of each row of the data/sequence. Must have the same length as the number of rows/sequences ofx. Alternatively, a singlecharacterstring giving the column name of the data that defines the group whenxis a wide formatdata.frameor atna_dataobject.- sub
An
integervector of subsequence lengths to analyze. The default is2:5.- min_freq
An
integergiving the minimum number of times that a specific pattern has to be observed to be included in the analysis. The default is5.- correction
A
characterstring 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()