Standard.configuration_peptide: Standard configuration for feature extraction including...
In crarlus/paprbag: Pathogenicity Prediction of Bacterial Genomes
Description
Usage
Format
Details
Description
Standard configuration for feature extraction including peptide features
Usage
1
Format
An object of class list of length 22.
Details
NT_kmax = 4
Symmetric = TRUE
Do.NTMotifs = FALSE
NTMotifs = NULL
AllowedMismatches = 1
bothStrands = TRUE
Do.SpacedWords = TRUE
k.spaced = 4
l.spaced = 6
SingleSpacerPattern = 0
combineSpacerPatterns = TRUE
Do.PeptideFeatures = TRUE
Do.MonoPep = TRUE
Do.DiPep = FALSE
Do.AAprops = FALSE
Do.AAindex = TRUE
AAindex_Selection = c("BROC820101","BUNA790103","CHOP780207","FAUJ880105","FINA910103","GEIM800103","GEIM800105","ISOY800107","KHAG800101","LEWP710101","MAXF760103","OOBM850104","PALJ810111","PRAM820103","QIAN880102","QIAN880114","QIAN880123","QIAN880137","RACS770103","RACS820103","RICJ880101","RICJ880117","ROBB760107","TANS770106","TANS770108","VASM830101","WERD780104","AURR980102","AURR980116","AURR980118","FUKS010109","SUYM030101")
Do.UCO = TRUE
Do.PepPatterns = FALSE
SearchPatternsSixFrame = FALSE
AllowedPeptideMismatches = 0
AggregatePatterns = FALSE
crarlus/paprbag documentation built on May 14, 2019, 11:31 a.m.
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Description Usage Format Details
Description
Standard configuration for feature extraction including peptide features
Usage
1 |
Format
An object of class list of length 22.
Details
NT_kmax = 4 Symmetric = TRUE Do.NTMotifs = FALSE NTMotifs = NULL AllowedMismatches = 1 bothStrands = TRUE Do.SpacedWords = TRUE k.spaced = 4 l.spaced = 6 SingleSpacerPattern = 0 combineSpacerPatterns = TRUE Do.PeptideFeatures = TRUE Do.MonoPep = TRUE Do.DiPep = FALSE Do.AAprops = FALSE Do.AAindex = TRUE AAindex_Selection = c("BROC820101","BUNA790103","CHOP780207","FAUJ880105","FINA910103","GEIM800103","GEIM800105","ISOY800107","KHAG800101","LEWP710101","MAXF760103","OOBM850104","PALJ810111","PRAM820103","QIAN880102","QIAN880114","QIAN880123","QIAN880137","RACS770103","RACS820103","RICJ880101","RICJ880117","ROBB760107","TANS770106","TANS770108","VASM830101","WERD780104","AURR980102","AURR980116","AURR980118","FUKS010109","SUYM030101") Do.UCO = TRUE Do.PepPatterns = FALSE SearchPatternsSixFrame = FALSE AllowedPeptideMismatches = 0 AggregatePatterns = FALSE
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