R: Feature Extraction from Biological Sequences

# Feature Extraction from Biological Sequences

## Documentation for package ‘ftrCOOL’ version 2.0.0

- DESCRIPTION file
- Package NEWS

## Help Pages

A B C D E F G K L M N O P Q R S T Z

## -- A --

AA2Binary | Amino Acid To Binary (AA2Binary)
AAindex | Amino Acid Index (AAindex)
AAKpartComposition | Amino Acid to K Part Composition (AAKpartComposition)
AAutoCor | Amino Acid Autocorrelation-Autocovariance (AAutoCor)
AESNN3 | Learn from alignments (AESNN3)
alphabetCheck | AlphabetCheck
ANF_DNA | Accumulated Nucleotide Frequency (ANF_DNA)
ANF_RNA | Accumulated riboNucleotide Frequency (ANF_RNA)
APAAC | Amphiphilic Pseudo-Amino Acid Composition(series) (APAAC)
APkNUCdi_DNA | Amphiphilic Pseudo-k Nucleotide Composition-di(series) (APkNUCdi_DNA)
APkNUCdi_RNA | Amphiphilic Pseudo-k riboNucleotide Composition-di(series) (APkNUCdi_RNA)
APkNUCTri_DNA | Amphiphilic Pseudo-k Nucleotide Composition-Tri(series) (APkNUCTri_DNA)
ASA | Accessible Solvent Accessibility (ASA)
ASDC | Adaptive skip dipeptide composition (ASDC)
ASDC_DNA | Adaptive skip dinucleotide composition_DNA) (ASDC_DNA)
ASDC_RNA | Adaptive skip di-ribonucleotide composition) (ASDC_RNA)
AutoCorDiNUC_DNA | Di Nucleotide Autocorrelation-Autocovariance (AutoCorDiNUC_DNA)
AutoCorDiNUC_RNA | Di riboNucleotide Autocorrelation-Autocovariance (AutoCorDiNUC_RNA)
AutoCorTriNUC_DNA | Tri Nucleotide Autocorrelation-Autocovariance (AutoCorTriNUC_DNA)

## -- B --

binary_3bit_T1 | Binary - 3bit - Type1 (binary_3bit_T1)
binary_3bit_T2 | Binary - 3bit - Type2 (binary_3bit_T2)
binary_3bit_T3 | Binary - 3bit - Type3 (binary_3bit_T3)
binary_3bit_T4 | Binary - 3bit - Type4 (binary_3bit_T4)
binary_3bit_T5 | Binary - 3bit - Type5 (binary_3bit_T5)
binary_3bit_T6 | Binary - 3bit - Type6 (binary_3bit_T6)
binary_3bit_T7 | Binary - 3bit - Type7 (binary_3bit_T7)
binary_5bit_T1 | Binary - 5bit - Type1 (binary_5bit_T1)
binary_5bit_T2 | Binary - 5bit - Type2 (binary_5bit_T2)
binary_6bit | Binary - 6bit (binary_6bit)
BLOSUM62 | Blosum62 (BLOSUM62)

## -- C --

CkSAApair | Composition of k-Spaced Amino Acids pairs (CkSAApair)
CkSGAApair | Composition of k-Spaced Grouped Amino Acids pairs (CkSGAApair)
CkSNUCpair_DNA | Composition of k-Spaced Nucleotides Pairs (CkSNUCpair_DNA)
CkSNUCpair_RNA | Composition of k-Spaced riboNucleotides Pairs (CkSNUCpair_RNA)
codonAdaptionIndex | Codon Adaption Index (codonAdaptionIndex)
CodonFraction | Codon Fraction (CodonFraction)
CodonUsage_DNA | Codon Usage in DNA (CodonUsage_DNA)
CodonUsage_RNA | Codon Usage in RNA (CodonUsage_RNA)
conjointTriad | Conjoint Triad (conjointTriad)
conjointTriadKS | k-Spaced Conjoint Triad (conjointTriadKS)
CTD | Composition_Transition_Distribution (CTD)
CTDC | CTD Composition (CTDC)
CTDD | CTD Distribution (CTDD)
CTDT | CTD Transition (CTDT)

## -- D --

DDE | Dipeptide Deviation from Expected Mean value (DDE)
DiNUC2Binary_DNA | Dinucleotide To Binary DNA (DiNUC2Binary_DNA)
DiNUC2Binary_RNA | Di riboNucleotide To Binary RNA (DiNUC2Binary_RNA)
DiNUCindex_DNA | Di Nucleotide Index (DiNUCindex_DNA)
DiNUCindex_RNA | Di riboNucleotide Index (DiNUCindex_RNA)
DisorderB | disorder Binary (DisorderB)
DisorderC | disorder Content (DisorderC)
DisorderS | disorder Simple (DisorderS)
DistancePair | PseAAC of distance-pairs and reduced alphabet (DistancePair)
DPCP_DNA | Dinucleotide physicochemical properties (DPCP_DNA)
DPCP_RNA | Di-ribonucleotide physicochemical properties (DPCP_RNA)

## -- E --

EAAComposition | Enhanced Amino Acid Composition (EAAComposition)
EffectiveNumberCodon | Effective Number of Codon (EffectiveNumberCodon)
EGAAComposition | Enhanced Grouped Amino Acid Composition (EGAAComposition)
EIIP | Electron-Ion Interaction Pseudopotentials (EIIP)
ENUComposition_DNA | Enhanced Nucleotide Composition (ENUComposition_DNA)
ENUComposition_RNA | Enhanced riboNucleotide Composition (ENUComposition_RNA)
ExpectedValKmerNUC_DNA | Expected Value for K-mer Nucleotide (ExpectedValKmerNUC_DNA)
ExpectedValKmerNUC_RNA | Expected Value for K-mer riboNucleotide (ExpectedValKmerNUC_RNA)
ExpectedValueAA | Expected Value for each Amino Acid (ExpectedValueAA)
ExpectedValueGAA | Expected Value for Grouped Amino Acid (ExpectedValueGAA)
ExpectedValueGKmerAA | Expected Value for Grouped K-mer Amino Acid(ExpectedValueGKmerAA)
ExpectedValueKmerAA | Expected Value for K-mer Amino Acid (ExpectedValueKmerAA)

## -- F --

fa.read | Fasta File Reader (fa.read)
fickettScore | Fickett Score (fickettScore)

## -- G --

GAAKpartComposition | Grouped Amino Acid K Part Composition (GAAKpartComposition)
GrpDDE | Group Dipeptide Deviation from Expected Mean (GrpDDE)
G_Ccontent_DNA | G_C content in DNA (G_Ccontent_DNA)
G_Ccontent_RNA | G_C content in RNA (G_Ccontent_RNA)

## -- K --

kAAComposition | k Amino Acid Composition (kAAComposition)
kGAAComposition | k Grouped Amino Acid Composition (kGAAComposition)
KNNPeptide | K-Nearest Neighbor for Peptides (KNNPeptide)
KNNProtein | K-Nearest Neighbor for Protein (KNNProtein)
KNN_DNA | K-Nearest Neighbor_DNA (KNN_DNA)
KNN_RNA | K-Nearest Neighbor_RNA (KNN_RNA)
kNUComposition_DNA | k Nucleotide Composition (kNUComposition_DNA)
kNUComposition_RNA | k riboNucleotide Composition (kNUComposition_RNA)

## -- L --

LocalPoSpKAAF | Local Position Specific k Amino Acids Frequency (LocalPoSpKAAF)
LocalPoSpKNUCF_DNA | Local Position Specific k Nucleotide Frequency (LocalPoSpKNUCF_DNA)
LocalPoSpKNUCF_RNA | Local Position Specific k riboNucleotide Frequency (LocalPoSpKNUCF_RNA)

## -- M --

maxORF | Maximum Open Reading Frame in DNA (maxORF)
maxORFlength_DNA | Maximum Open Reading Frame length in DNA (maxORFlength_DNA)
maxORFlength_RNA | Maximum Open Reading Frame length in RNA (maxORFlength_RNA)
maxORF_RNA | Maximum Open Reading Frame in RNA (maxORF_RNA)
Mismatch_DNA | Mismatch_DNA (Mismatch_DNA)
Mismatch_RNA | Mismatch_RNA (Mismatch_RNA)
MMI_DNA | Multivariate Mutual Information_DNA (MMI_DNA)
MMI_RNA | Multivariate Mutual Information_RNA (MMI_RNA)

## -- N --

nameKmer | naming Kmer (nameKmer)
NCP_DNA | Nucleotide Chemical Property (NCP_DNA)
NCP_RNA | riboNucleotide Chemical Property (NCP_RNA)
needleman | Needleman-Wunsch (needleman)
nonStandardSeq | nonStandard sequence (nonStandardSeq)
NUC2Binary_DNA | Nucleotide To Binary (NUC2Binary_DNA)
NUC2Binary_RNA | riboNucleotide To Binary (NUC2Binary_RNA)
NUCKpartComposition_DNA | Nucleotide to K Part Composition (NUCKpartComposition_DNA)
NUCKpartComposition_RNA | riboNucleotide to K Part Composition (NUCKpartComposition_RNA)

## -- O --

OPF_10bit | Overlapping Property Features_10bit (OPF_10bit)
OPF_7bit_T1 | Overlapping property features_7bit_T1 (OPF_7bit_T1)
OPF_7bit_T2 | Overlapping property features_7bit_T2 (OPF_7bit_T2)
OPF_7bit_T3 | Overlapping property features_7bit_T3 (OPF_7bit_T3)

## -- P --

PCPseDNC | Parallel Correlation Pseudo Dinucleotide Composition (PCPseDNC)
PS2_DNA | Position-specific of two nucleotide_DNA (PS2_DNA)
PS2_RNA | Position-specific of two nucleotide_RNA (PS2_RNA)
PS3_DNA | Position-specific of three nucleotide_DNA (PS3_DNA)
PS3_RNA | Position-specific of three ribonucleotide_RNA (PS3_RNA)
PS4_DNA | Position-specific of four nucleotide_DNA (PS4_DNA)
PS4_RNA | Position-specific of four ribonucleotide (PS4_RNA)
PSEAAC | Pseudo-Amino Acid Composition (Parallel) (PSEAAC)
PseEIIP | Pseudo Electron-Ion Interaction Pseudopotentials of Trinucleotide (PseEIIP)
PSEkNUCdi_DNA | Pseudo k Nucleotide Composition-Di(Parallel) (PSEkNUCdi_DNA)
PSEkNUCdi_RNA | Pseudo k riboNucleotide Composition-Di(Parallel) (PSEkNUCdi_RNA)
PSEkNUCTri_DNA | Pseudo k Nucleotide Composition-Tri(Parallel) (PSEkNUCTri_RNA)
PseKRAAC_T1 | Pseudo K_tuple Reduced Amino Acid Composition Type-1 (PseKRAAC_T1)
PseKRAAC_T10 | Pseudo K_tuple Reduced Amino Acid Composition Type-10 (PseKRAAC_T10)
PseKRAAC_T11 | Pseudo K_tuple Reduced Amino Acid Composition Type-11 (PseKRAAC_T11)
PseKRAAC_T12 | Pseudo K_tuple Reduced Amino Acid Composition Type-12 (PseKRAAC_T12)
PseKRAAC_T13 | Pseudo K_tuple Reduced Amino Acid Composition Type_13 (PseKRAAC_T13)
PseKRAAC_T14 | Pseudo K_tuple Reduced Amino Acid Composition Type-14 (PseKRAAC_T14)
PseKRAAC_T15 | Pseudo K_tuple Reduced Amino Acid Composition Type-15 (PseKRAAC_T15)
PseKRAAC_T16 | Pseudo K_tuple Reduced Amino Acid Composition Type-16 (PseKRAAC_T16)
PseKRAAC_T2 | Pseudo K_tuple Reduced Amino Acid Composition Type-2 (PseKRAAC_T2)
PseKRAAC_T3A | Pseudo K_tuple Reduced Amino Acid Composition Type-3A (PseKRAAC_T3A)
PseKRAAC_T3B | Pseudo K_tuple Reduced Amino Acid Composition Type_3B (PseKRAAC_T3B)
PseKRAAC_T4 | Pseudo K_tuple Reduced Amino Acid Composition Type-4 (PseKRAAC_T4)
PseKRAAC_T5 | Pseudo K_tuple Reduced Amino Acid Composition Type-5 (PseKRAAC_T5)
PseKRAAC_T6A | Pseudo K_tuple Reduced Amino Acid Composition Type-6A (PseKRAAC_T6A)
PseKRAAC_T6B | Pseudo K_tuple Reduced Amino Acid Composition Type-6B (PseKRAAC_T6B)
PseKRAAC_T7 | Pseudo K_tuple Reduced Amino Acid Composition Type-7 (PseKRAAC_T7)
PseKRAAC_T8 | Pseudo K_tuple Reduced Amino Acid Composition Type-8 (PseKRAAC_T8)
PseKRAAC_T9 | Pseudo K_tuple Reduced Amino Acid Composition Type-9 (PseKRAAC_T9)
PSSM | Position-Specific Scoring Matrix (PSSM)
PSTNPds | Position-Specific Trinucleotide Propensity based on double-strand (PSTNPds)
PSTNPss_DNA | Position-Specific Trinucleotide Propensity based on single-strand DNA (PSTNPss_DNA)
PSTNPss_RNA | Position-Specific Tri-ribonucleotide Propensity based on single-strand RNA (PSTNPss_RNA)

## -- Q --

QSOrder | Quasi Sequence Order (QSOrder)

## -- R --

readASAdir | Read Directory of Accessible Solvent accessibility predicted files (readASAdir)
readDisDir | Read disorder predicted Directory (readDisDir)
readPSSMdir | Read PSSM Directory (readPSSMdir)
readss2Dir | Read ss2 predicted Directory (readss2Dir)
readTorsionDir | Read Directory of Torsion predicted files (readTorsionDir)
revComp | reverseCompelement (revComp)

## -- S --

SAAC | Splitted Amino Acid Composition (SAAC)
SGAAC | Splitted Group Amino Acid Composition (SGAAC)
SOCNumber | Sequence Order Coupling Number (SOCNumber)
SSEB | Secondary Structure Elements Binary (SSEB)
SSEC | Secondary Structure Elements Composition (SSEC)
SSES | Secondary Structure Elements Simple (SSES)

## -- T --

TorsionAngle | Torsion Angle (TorsionAngle)
TPCP_DNA | Trinucleotide physicochemical properties (TPCP_DNA)
TriNUCindex_DNA | Tri Nucleotide Index (TriNucIndex)

## -- Z --

Zcurve12bit_DNA | Z_curve_12bit_DNA (Zcurve12bit_DNA)
Zcurve12bit_RNA | Z_curve_12bit_RNA (Zcurve12bit_RNA)
Zcurve144bit_DNA | Z_curve_144bit_DNA (Zcurve144bit_DNA)
Zcurve144bit_RNA | Z_curve_144bit_RNA (Zcurve144bit_RNA)
Zcurve36bit_DNA | Z_curve_36bit_DNA (Zcurve36bit_DNA)
Zcurve36bit_RNA | Z_curve_36bit_RNA (Zcurve36bit_RNA)
Zcurve48bit_DNA | Z_curve_48bit_DNA (Zcurve48bit_DNA)
Zcurve48bit_RNA | Z_curve_48bit_RNA (Zcurve48bit_RNA)
Zcurve9bit_DNA | Z_curve_9bit_DNA (Zcurve9bit_DNA)
Zcurve9bit_RNA | Z_curve_9bit_RNA (Zcurve9bit_RNA)
zSCALE | Z-SCALE (zSCALE)