BALCONY (version 0.2.10)

create_final_CSV: Create CSV file to save results

Description

Create_final_CSV() saves results as table into csv file. Combination of given variation allows to compare protein structure with evolutionary data content from alignment. Each position on alignment has its own column in csv file. If the length of the alignmnet exceeds 1000 characters, the output is divided into separate files with suffixes corresponing to the number of file produced by this function.

Usage

create_final_CSV(filename,variations_matrix,structure,sequence_id,alignment,score_list)

Arguments

filename

name of the output file produced by the function

variations_matrix

An object which contains alignment and frequencies of occurences each amino acids on each position of alignment. Output of calculate_AA_variation

structure

An strcture object - matrix of aligned, examined protein sequence covered by structure markers (S/N). Output of create_structure_seq.

sequence_id

the Uniprot code of the sequence of interest

alignment

the output of read.alignment function. A variable containing alignment data. One of the sequences must be the sequence of interest

score_list

list of calculated entropy/conservation scores. Optional parameter. If not provided, this rows are not present in the output file

Value

csv_file

A comma separated variable file containing information provided to this function. It is also written in the current directory.

See Also

create_structure_seq, schneider_conservativity, Escore_conservativity, landgraf_conservativity, read.alignment

Examples

# NOT RUN {
data("alignment")
data("structure")
uniprot="P34914"
alignment = delete_isoforms(alignment)
threshold = 1
# }
# NOT RUN {
var_aa=calculate_AA_variation(alignment,threshold)
entropy_data=list(Schneider.entropy=schneider_conservativity(alignment),
                  Escore.entropy = Escore_conservativity(alignment))
create_final_CSV("my_filename",var_aa,structure,uniprot,alignment,entropy_data)
# }