ftrCOOL (version 2.0.0)

ASA: Accessible Solvent Accessibility (ASA)

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.

Examples

# NOT RUN {
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)
# }