getfreqs {SeqFeatR}

Get frequencies for amino acids/nucleotides in alignment window (epitope)

Description

Gets frequencies of amino acids/nucleotides inside an epitope out of an alignment. Epitope start and end positions must be in the range of the length of the alignment, starting with the first position of the alignment as one. You can add the whole sequence consensus, but also a part of it.

Usage

getfreqs(path_to_file_sequence_alignment = NULL, save_csv, save_png, 
 epitope_position_start, epitope_position_end,
 path_to_file_consensus, patnum_threshold = 1, A11, A12, A21, A22,
 B11, B12, B21, B22, one_feature=FALSE)

Arguments

path_to_file_sequence_alignment

a FASTA file with sequence data. For reference please look in example file.

save_csv

name for the csv output.

save_png

name for the png/svg output.

epitope_position_start

starting position of the epitope in the alignment.

epitope_position_end

ending position of the epitope in the alignment.

path_to_file_consensus

a FASTA file with the consensus sequence from epi_pos_start till epi_pos_end.

patnum_threshold

the minimum number of patients of one HLA type to consider in the calculation.

A11

the position of the start of the first HLA A allele in the description block of the FASTA file.

A12

the position of the end of the first HLA A allele in the description block of the FASTA file.

A21

the position of the start of the second HLA A allele in the description block of the FASTA file.

A22

the position of the end of the second HLA A allele in the description block of the FASTA file.

B11

the position of the start of the first HLA B allele in the description block of the FASTA file.

B12

the position of the end of the first HLA B allele in the description block of the FASTA file.

B21

the position of the start of the second HLA B allele in the description block of the FASTA file.

B22

the position of the end of the second HLA B allele in the description block of the FASTA file.

one_feature

if there is only one feature.

Details

This function counts the number of amino acids NOT being the same as the consensus and generates an output graphic as well as a result csv file.

The 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). For non-HLA-type features, set option one_feature=TRUE. The value of the feature (e.g. 'yes / no', or '1 / 2 / 3') should then be given at the end of each FASTA comment, separated from the part before that by a semicolon.

Value

A csv file with a row for each feature and two columns (absolute and relative) for the frequencies of the amino acids in the epitope.

Author(s)

Bettina Budeus

See Also

assocpoint

Examples

#Input files
	fasta_input <- system.file("extdata", "Example_aa.fasta", package="SeqFeatR")
	consensus_input <- system.file("extdata", "Example_Consensus_aa.fasta", package="SeqFeatR")
	
#Usage
getfreqs(
	path_to_file_sequence_alignment=fasta_input,
	save_csv="getfreqs_result.csv",
	save_png="getfreqs_result.png",
	epitope_position_start=1,
	epitope_position_end=40,
	path_to_file_consensus=consensus_input,
	patnum_threshold=1,
	A11=10,
	A12=11,
	A21=13,
	A22=14,
	B11=17,
	B12=18,
	B21=20,
	B22=21,
	one_feature=FALSE)