FASTA file with sequence alignment. See example file.
path_to_file_consensus
FASTA file with consensus sequence. See example file.
save_name_csv
name of file to which results are written in csv format.
dna
indicates whether sequences are DNA or amino acids.
significance_level
significance level for Fisher's exact test.
multiple_testing_correction
multiple testing correction applied to p-values. Input can be: "holm",
"hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none".
Details
For every position in the sequence alignment from the FASTA
file a Fisher's exact test is applied with every other position in the
sequence to check whether at both positions we have correlated
mutations with respect to a given consensus sequence. Significant p-values are
collected in one big table. p.adjust from stats package is used for multiple testing
correction; corrected values are given as extra column in csv output.
In contrast to assocpairfeat, assocpair does not use features, but uses a consensus
approach. Please be sure, that this is really what you want to use. Otherwise, use
assocpairfeat or assoctuple instead.
Value
A csv file with every possible co-mutation below the given p-value.