assocpointpair {SeqFeatR}

Compare results of SeqFeatRs assocpoint with SeqFeatRs assocpair, assocpairfeat

Description

Calculates which significant positions in result of assocpoint are also in results of assocpair/assocpairfeat.

Usage

assocpointpair(path_to_file_sequence_alignment = NULL, 
    path_to_file_assocpoint_csv_result = NULL, 
    path_to_file_assocpairfeat_csv_result = NULL,
    significance_level = 0.05, save_name_csv, save_name_pos)

Arguments

path_to_file_sequence_alignment

FASTA file with sequence alignment. For reference see example file.

path_to_file_assocpoint_csv_result

file with result from SeqFeatRs assocpoint. For reference see example file.

path_to_file_assocpairfeat_csv_result

file with results from SeqFeatRs assocpair, assocpairfeat. For reference see example file.

significance_level

p-value to be defined as significant.

save_name_csv

name of file to which results are saved in csv format.

save_name_pos

name of file to which results are saved in csv format (contains possible compensatory mutations).

Details

Takes the results from assocpoint and assocpair/assocpairfeat and tries to combine them into one result: we are looking for pairs of sequence alignment positions where (a) each of the positions is significantly associated with the feature (for significance level see parameter significance_level), and (b) the sequence states of both positions are associated. Pairs of positions fulfilling these two criteria may e.g. carry compensatory mutations. If at least one such mutation is found, a detailed output is additionally created with possible compensatory mutations

Value

A csv file with p-value for alignment position pairs and if existing a csv file with possible compensatory mutations.

Author(s)

Bettina Budeus

See Also

assocpoint

assocpairfeat

assocpair

Examples

#Input files
fasta_input <- system.file("extdata", "Example_aa.fasta", package="SeqFeatR")
assocpoint_result <- system.file("extdata", "assocpoint_results.csv", package="SeqFeatR")
assocpairfeat_result <- system.file("extdata", "assocpairfeat_results.csv", package="SeqFeatR")

#Usage
assocpointpair(
	path_to_file_sequence_alignment=fasta_input, 
	path_to_file_assocpoint_csv_result=assocpoint_result, 
	path_to_file_assocpairfeat_csv_result=assocpairfeat_result, 
	significance_level=0.05,
	save_name_csv="assocpointpair_result.csv",
	save_name_pos="possible_compensatory_mutation.csv")