ASA: Accessible Solvent Accessibility (ASA)

In ftrCOOL: Feature Extraction from Biological Sequences

Description

ASA represents an amino acid by a numeric value. This function extracts the ASA from the output of SPINE-X software which predicts ASA for each amino acid in a peptide or protein sequence. The output of SPINE-X is a tab-delimited file. ASAs are in the 11th column of the file.

Usage

ASA(dirPath, outFormat = "mat", outputFileDist = "")

Arguments

dirPath	Path of the directory which contains all output files of SPINE-X. Each file belongs to a sequence.
outFormat	It can take two values: 'mat' (which stands for matrix) and 'txt'. The default value is 'mat'.
outputFileDist	It shows the path and name of the 'txt' output file.

Value

The output depends on the outFormat which can be either 'mat' or 'txt'. If outFormat is 'mat', the function returns a feature matrix for sequences with the same lengths such that the number of columns is equal to the length of the sequences and the number of rows is equal to the number of sequences. If the outFormat is 'txt', the output is written to a tab-delimited file.

Note

This function is provided for sequences with the same lengths. Users can use 'txt' option in outFormat for sequences with different lengths. Warning: If outFormat is set to 'mat' for sequences with different lengths, it returns an error. Also, when output format is 'txt', label information is not shown in the text file. It is noteworthy that 'txt' format is not usable for machine learning purposes if sequences have different sizes. Otherwise 'txt' format is also usable for machine learning purposes.

Examples

dir = tempdir()
ad<-paste0(dir,"/asa.txt")


PredASAdir<-system.file("testForder",package="ftrCOOL")
PredASAdir<-paste0(PredASAdir,"/ASAdir/")
ASA(PredASAdir,outFormat="txt",outputFileDist=ad)

unlink("dir", recursive = TRUE)

ftrCOOL documentation built on Nov. 30, 2021, 1:07 a.m.