comparewithancestral {SeqFeatR}

Compares ancestral sequence with sequence alignment

Description

Generates from a nexus tree file the possible ancestral sequence and compares this with the sequence alignment.

Usage

comparewithancestral(path_to_file_sequence_alignment = NULL,
    path_to_file_nexus_tree = NULL, save_name_csv, 
    patnum_threshold = 1, significance_level = 0.05,
    A11, A12, A21, A22, B11, B12, B21, B22)

Arguments

path_to_file_sequence_alignment

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

path_to_file_nexus_tree

nexus tree file of sequences alignment. For reference see example file.

save_name_csv

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

patnum_threshold

minimum number of patients per HLA type to consider in calculation.

significance_level

significance level in Fisher's exact test.

A11

position of start of first HLA A allele in header line of FASTA file.

A12

position of end of first HLA A allele in header line of FASTA file.

A21

position of start of second HLA A allele in header line of FASTA file.

A22

position of end of second HLA A allele in header line of FASTA file.

B11

position of start of first HLA B allele in header line of FASTA file.

B12

position of end of first HLA B allele in header line of FASTA file.

B21

position of start of second HLA B allele in header line of FASTA file.

B22

position of end of second HLA B allele in header line of FASTA file.

Details

Features may be HLA types, indicated by four blocks in the FASTA comment lines. The positions of these blocks in the comment lines are defined by parameters A11, ..., B22. For patients with a homozygous HLA allele the second allele has to be "00" (without the double quotes).

Uses the R-packages ape and phangorn to create from a given nexus tree file the ancestral sequence. For every sequence position the ancestral amino acid is compared with the amino acid of every HLA type and with a Fisher's exact test the significant differences are calculated.

Value

Generates a csv file with p-values and q-values (generated by the R-package qvalue) for every HLA type and sequence position with a p-value below given threshold (significance_level).

Note

BEWARE! You have to name the FASTA sequences (= comment line in the file) so that the R-packages ape and phangorn can read and write them correctly. It will replace any space character with "_" (without the double quotes) and ignore ":" (without the double quotes)!

Author(s)

Bettina Budeus

Examples

#Input files
## Not run: 
fasta_input <- system.file("extdata", "Example_aa_for_cwa.fasta", package="SeqFeatR")
tree_input <- system.file("extdata", "Example_tree.nh", package="SeqFeatR")

#Usage
comparewithancestral(
	path_to_file_sequence_alignment=fasta_input,
	path_to_file_nexus_tree=tree_input,
	save_name_csv="hlaTree_results.csv",
	patnum_threshold=1,
	significance_level=0.05,
	A11=10,
	A12=11,
	A21=13,
	A22=14,
	B11=17,
	B12=18,
	B21=20,
	B22=21)

## End(Not run)