foundereffectfinder {SeqFeatR}

Tries to identify a founder effect in results from SeqFeatRs assocpair

Description

Takes the result of co-mutation analysis like SeqFeatRs assocpair function and adds a column with a note if the row is in the same branch.

Usage

foundereffectfinder(path_to_file_sequence_alignment = NULL,
    path_to_file_assocpair_csv_result = NULL, path_to_file_nexus_tree = NULL,
    save_name_csv, threshold = 7)

Arguments

path_to_file_sequence_alignment

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

path_to_file_assocpair_csv_result

csv file with results from SeqFeatRs assocpair function. For reference see example file.

path_to_file_nexus_tree

nexus file with tree data for the given sequence alignment. For reference see example file.

save_name_csv

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

threshold

threshold for the number of allowed occurrences of tips in one branch.

Details

Uses the results from SeqFeatRs assocpair analysis and a generated tree for the same sequences in nexus format (for tree generation, e.g http://mafft.cbrc.jp/alignment/server/ can be used). For every pair of amino acids the number of sequences with both amino acids inside one branch is calculated. If this number exceeds 'threshold' times the number of found associations, this association is considered to be due to a founder effect.

Value

Input file with an added column with founder effect information.

Note

Only use files generated with SeqFeatRs assocpair or assoctuple.

Author(s)

Bettina Budeus

References

Mayr, Ernst (1954). "Change of genetic environment and evolution". In Julian Huxley. Evolution as a Process. London: George Allen & Unwin. OCLC 974739

See Also

assocpair

Examples

#Input files
fasta_input <- system.file("extdata", "Example_aa.fasta", package="SeqFeatR")
assocpair_result <- system.file("extdata", "assocpair_results.csv", package="SeqFeatR")
tree_input <- system.file("extdata", "Example_tree.nh", package="SeqFeatR")

#Usage
foundereffectfinder(
	path_to_file_sequence_alignment=fasta_input,
	path_to_file_assocpair_csv_result=assocpair_result,
	path_to_file_nexus_tree=tree_input,
	save_name_csv="foundereffectfinder_result.csv",
	threshold=7)