extractDC: Dipeptide Composition Descriptor

Description Usage Arguments Value Author(s) References See Also Examples

View source: R/desc-02-DC.R

Description

This function calculates the Dipeptide Composition descriptor (dim: 400).

Usage

1

Arguments

x

A character vector, as the input protein sequence.

Value

A length 400 named vector

Author(s)

Nan Xiao <https://nanx.me>

References

M. Bhasin, G. P. S. Raghava. Classification of Nuclear Receptors Based on Amino Acid Composition and Dipeptide Composition. Journal of Biological Chemistry, 2004, 279, 23262.

See Also

See extractAAC and extractTC for Amino Acid Composition and Tripeptide Composition descriptors.

Examples

1
2
x = readFASTA(system.file("protseq/P00750.fasta", package = "protr"))[[1]]
extractDC(x)

Example output

         AA          RA          NA          DA          CA          EA 
0.003565062 0.003565062 0.000000000 0.007130125 0.003565062 0.003565062 
         QA          GA          HA          IA          LA          KA 
0.007130125 0.007130125 0.001782531 0.003565062 0.001782531 0.001782531 
         MA          FA          PA          SA          TA          WA 
0.000000000 0.005347594 0.003565062 0.007130125 0.003565062 0.000000000 
         YA          VA          AR          RR          NR          DR 
0.000000000 0.000000000 0.003565062 0.007130125 0.005347594 0.001782531 
         CR          ER          QR          GR          HR          IR 
0.005347594 0.005347594 0.000000000 0.007130125 0.001782531 0.003565062 
         LR          KR          MR          FR          PR          SR 
0.005347594 0.001782531 0.001782531 0.003565062 0.001782531 0.003565062 
         TR          WR          YR          VR          AN          RN 
0.003565062 0.000000000 0.005347594 0.003565062 0.001782531 0.003565062 
         NN          DN          CN          EN          QN          GN 
0.000000000 0.005347594 0.001782531 0.000000000 0.001782531 0.005347594 
         HN          IN          LN          KN          MN          FN 
0.003565062 0.000000000 0.003565062 0.001782531 0.000000000 0.001782531 
         PN          SN          TN          WN          YN          VN 
0.000000000 0.001782531 0.003565062 0.003565062 0.000000000 0.000000000 
         AD          RD          ND          DD          CD          ED 
0.003565062 0.005347594 0.003565062 0.003565062 0.001782531 0.001782531 
         QD          GD          HD          ID          LD          KD 
0.000000000 0.005347594 0.001782531 0.001782531 0.001782531 0.001782531 
         MD          FD          PD          SD          TD          WD 
0.001782531 0.001782531 0.007130125 0.005347594 0.001782531 0.000000000 
         YD          VD          AC          RC          NC          DC 
0.001782531 0.000000000 0.003565062 0.005347594 0.000000000 0.001782531 
         CC          EC          QC          GC          HC          IC 
0.003565062 0.003565062 0.003565062 0.001782531 0.001782531 0.001782531 
         LC          KC          MC          FC          PC          SC 
0.007130125 0.001782531 0.000000000 0.001782531 0.000000000 0.007130125 
         TC          WC          YC          VC          AE          RE 
0.005347594 0.005347594 0.007130125 0.005347594 0.003565062 0.000000000 
         NE          DE          CE          EE          QE          GE 
0.000000000 0.001782531 0.003565062 0.003565062 0.005347594 0.003565062 
         HE          IE          LE          KE          ME          FE 
0.001782531 0.000000000 0.000000000 0.003565062 0.000000000 0.001782531 
         PE          SE          TE          WE          YE          VE 
0.001782531 0.007130125 0.003565062 0.001782531 0.001782531 0.003565062 
         AQ          RQ          NQ          DQ          CQ          EQ 
0.008912656 0.001782531 0.000000000 0.001782531 0.005347594 0.001782531 
         QQ          GQ          HQ          IQ          LQ          KQ 
0.003565062 0.001782531 0.001782531 0.000000000 0.003565062 0.000000000 
         MQ          FQ          PQ          SQ          TQ          WQ 
0.000000000 0.001782531 0.003565062 0.005347594 0.001782531 0.001782531 
         YQ          VQ          AG          RG          NG          DG 
0.003565062 0.000000000 0.005347594 0.007130125 0.003565062 0.003565062 
         CG          EG          QG          GG          HG          IG 
0.007130125 0.003565062 0.003565062 0.008912656 0.000000000 0.001782531 
         LG          KG          MG          FG          PG          SG 
0.010695187 0.001782531 0.000000000 0.001782531 0.005347594 0.012477718 
         TG          WG          YG          VG          AH          RH 
0.000000000 0.001782531 0.001782531 0.001782531 0.003565062 0.000000000 
         NH          DH          CH          EH          QH          GH 
0.001782531 0.000000000 0.003565062 0.000000000 0.003565062 0.000000000 
         HH          IH          LH          KH          MH          FH 
0.001782531 0.001782531 0.001782531 0.005347594 0.000000000 0.000000000 
         PH          SH          TH          WH          YH          VH 
0.001782531 0.001782531 0.001782531 0.000000000 0.000000000 0.001782531 
         AI          RI          NI          DI          CI          EI 
0.003565062 0.001782531 0.000000000 0.003565062 0.000000000 0.003565062 
         QI          GI          HI          II          LI          KI 
0.000000000 0.005347594 0.000000000 0.001782531 0.003565062 0.000000000 
         MI          FI          PI          SI          TI          WI 
0.003565062 0.000000000 0.000000000 0.000000000 0.000000000 0.003565062 
         YI          VI          AL          RL          NL          DL 
0.001782531 0.003565062 0.008912656 0.007130125 0.001782531 0.001782531 
         CL          EL          QL          GL          HL          IL 
0.005347594 0.001782531 0.003565062 0.010695187 0.003565062 0.007130125 
         LL          KL          ML          FL          PL          SL 
0.007130125 0.000000000 0.001782531 0.001782531 0.001782531 0.001782531 
         TL          WL          YL          VL          AK          RK 
0.001782531 0.001782531 0.001782531 0.005347594 0.003565062 0.000000000 
         NK          DK          CK          EK          QK          GK 
0.000000000 0.000000000 0.000000000 0.003565062 0.005347594 0.008912656 
         HK          IK          LK          KK          MK          FK 
0.001782531 0.001782531 0.005347594 0.000000000 0.001782531 0.001782531 
         PK          SK          TK          WK          YK          VK 
0.000000000 0.001782531 0.001782531 0.000000000 0.000000000 0.001782531 
         AM          RM          NM          DM          CM          EM 
0.001782531 0.001782531 0.003565062 0.000000000 0.000000000 0.000000000 
         QM          GM          HM          IM          LM          KM 
0.001782531 0.000000000 0.000000000 0.000000000 0.000000000 0.000000000 
         MM          FM          PM          SM          TM          WM 
0.000000000 0.000000000 0.000000000 0.001782531 0.000000000 0.000000000 
         YM          VM          AF          RF          NF          DF 
0.000000000 0.000000000 0.000000000 0.005347594 0.000000000 0.001782531 
         CF          EF          QF          GF          HF          IF 
0.003565062 0.003565062 0.001782531 0.001782531 0.000000000 0.001782531 
         LF          KF          MF          FF          PF          SF 
0.001782531 0.001782531 0.000000000 0.000000000 0.001782531 0.000000000 
         TF          WF          YF          VF          AP          RP 
0.000000000 0.000000000 0.003565062 0.003565062 0.000000000 0.005347594 
         NP          DP          CP          EP          QP          GP 
0.005347594 0.000000000 0.001782531 0.001782531 0.001782531 0.003565062 
         HP          IP          LP          KP          MP          FP 
0.001782531 0.000000000 0.005347594 0.005347594 0.000000000 0.001782531 
         PP          SP          TP          WP          YP          VP 
0.003565062 0.005347594 0.001782531 0.000000000 0.001782531 0.007130125 
         AS          RS          NS          DS          CS          ES 
0.003565062 0.007130125 0.007130125 0.005347594 0.007130125 0.005347594 
         QS          GS          HS          IS          LS          KS 
0.001782531 0.001782531 0.003565062 0.005347594 0.005347594 0.003565062 
         MS          FS          PS          SS          TS          WS 
0.000000000 0.001782531 0.007130125 0.010695187 0.001782531 0.001782531 
         YS          VS          AT          RT          NT          DT 
0.007130125 0.001782531 0.001782531 0.005347594 0.000000000 0.005347594 
         CT          ET          QT          GT          HT          IT 
0.003565062 0.000000000 0.000000000 0.005347594 0.000000000 0.000000000 
         LT          KT          MT          FT          PT          ST 
0.005347594 0.001782531 0.001782531 0.000000000 0.000000000 0.005347594 
         TT          WT          YT          VT          AW          RW 
0.000000000 0.001782531 0.003565062 0.003565062 0.000000000 0.000000000 
         NW          DW          CW          EW          QW          GW 
0.001782531 0.003565062 0.003565062 0.000000000 0.000000000 0.000000000 
         HW          IW          LW          KW          MW          FW 
0.000000000 0.000000000 0.000000000 0.000000000 0.000000000 0.000000000 
         PW          SW          TW          WW          YW          VW 
0.007130125 0.003565062 0.003565062 0.000000000 0.000000000 0.000000000 
         AY          RY          NY          DY          CY          EY 
0.001782531 0.000000000 0.005347594 0.000000000 0.005347594 0.003565062 
         QY          GY          HY          IY          LY          KY 
0.001782531 0.001782531 0.000000000 0.001782531 0.003565062 0.003565062 
         MY          FY          PY          SY          TY          WY 
0.000000000 0.001782531 0.001782531 0.003565062 0.003565062 0.000000000 
         YY          VY          AV          RV          NV          DV 
0.000000000 0.003565062 0.001782531 0.003565062 0.000000000 0.003565062 
         CV          EV          QV          GV          HV          IV 
0.001782531 0.001782531 0.001782531 0.001782531 0.003565062 0.001782531 
         LV          KV          MV          FV          PV          SV 
0.003565062 0.003565062 0.000000000 0.003565062 0.003565062 0.003565062 
         TV          WV          YV          VV 
0.005347594 0.000000000 0.001782531 0.003565062 

protr documentation built on Nov. 18, 2017, 9:03 a.m.