ftrCOOL (version 2.0.0)

PSSM: Position-Specific Scoring Matrix (PSSM)

Description

This functions receives as input PSSM matrices (which are created by PSI-BLAST software) and converts them into feature vectors.

Usage

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

Arguments

dirPath

Path of the directory which contains all output files of PSI-BLAST. 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 parameter which can be either 'mat' or 'txt'. If outFormat is 'mat', the function returns a feature matrix for sequences with the same length such that the number of columns is (sequence length)*(20) 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,"/pssm.txt")

PSSMdir<-system.file("testForder",package="ftrCOOL")
PSSMdir<-paste0(PSSMdir,"/PSSMdir/")
mat<-PSSM(PSSMdir,outFormat="txt",outputFileDist=ad)


unlink("dir", recursive = TRUE)
# }