CreateFeaturesFromReads: Create features from reads

In crarlus/paprbag: Pathogenicity Prediction of Bacterial Genomes

Description

This function extracts all kind of different features from a set of DNA sequences

Usage

CreateFeaturesFromReads(Reads, NT_kmax = 4, SymmetricFeatures = T,
  Do.NTMotifs = F, NTMotifs = NULL, AllowedMismatches = 0,
  bothStrands = T, Do.SpacedWords = T, k.spaced = 4, l.spaced = 6,
  Do.PeptideFeatures = T, Do.MonoPep = T, Do.DiPep = T, Do.AAprops = T,
  Do.AAindex = T, AAindex_Selection = NULL, Do.UCO = T,
  Do.PepPatterns = F, Patterns = NULL, SearchPatternsSixFrame = F,
  AllowedPeptideMismatches = 0, AggregatePatterns = F)

Arguments

Reads	A DNAStringSet object
Do.NTMotifs	Should features based on specified (genomic) sequence motifs (see NTMotifs) be computed
NTMotifs	Vector of characters containing the sequence motifs
AllowedMismatches	How many Mismatches are allowed for the motif search
bothStrands	Should the motifs be search on both strands?
Do.SpacedWords	Should the occurrence of spaced words be computed?
k.spaced	Specify the word length
l.spaced	Specify the word length including spacers
Do.PeptideFeatures	Should the DNA sequence be translated and peptide features be computed?
Do.DiPep	Should the monopeptide frequency be computed?
Do.AAprops	Should the amino acid properties be computed?
Do.AAindex	Should properties based on the AAindex stats be computed?
AAindex_Selection	Which AAindex properties should be computed: Vector of accession numbers
Do.UCO	Should the codon usage frequency be computed?
Do.PepPatterns	Should peptide pattern counts be computed?
Patterns	A vector of charaters for the peptide pattern search
SearchPatternsSixFrame	Should the patterns be searched in all 6 frames?
AggregatePatterns	Should the indidual patterns be aggregated into a single column?
Do.DiPep	Should the dipeptide frequency be computed?

Details

Make Stats from DNAString object, based on nucleotide sequence itself and the best translation into an amino acid sequence

Value

A data.frame containing the different features as columns. Each row repesents a DNA-string

Author(s)

Carlus Deneke

Examples

data(ReadData)
CreateFeaturesFromReads (Reads = ReadData,NT_kmax = 3)

crarlus/paprbag documentation built on May 14, 2019, 11:31 a.m.