basic: Assistant Functions
In BioSeqClass: Classification for Biological Sequences

Description Usage Arguments Details Author(s) Examples

Assistant functions including read/write files, invoke perl programs, and so on.

  ## Elements and groups of base and amino acid
  elements(ele.type)
  aaClass(aa.type)    

  pwm(seq,class=elements("aminoacid"))
  
  .pathPerl(perlName, os)
  .callPerl(perlName, os)  
  
  data(dssp.ss)
  data(aa.index)
  data(PROPERTY)
  data(DiProDB)

`ele.type`	a string for the type of biological sequence. This must be one of the strings "rnaBase", "dnaBase", "aminoacid" or "aminoacid2".
`aa.type`	a string for the group of amino acids. This must be one of the strings "aaH", "aaV", "aaZ", "aaP", "aaF", "aaS" or "aaE".
`seq`	a string vector for the protein or gene sequences.
`class`	a list for the class of biological properties. It can be produced by `elements` and `aaClass`.
`perlName`	a character string for the name of perl program.
`os`	character string, giving the Operating System (family) of the computer.

elements returns a list of basic elements of biological sequence. Parameter "ele.type" supported following selection: "rnaBase" - basic elements of RNA (ATCG). "dnaBase" - basic elements of DNA (AUCG). "aminoacid" - 20 amino acides (RKEDQNWGASTPHYCVLIMF). "aminoacid2" - 20 amino acides and 1 pseudo amino acid "O" (RKEDQNWGASTPHYCVLIMFO). Unknown or uncomplete amino acides will be substituted by pseudo amino acid.

aaClass returns a list of amino acids groups depend on their physical-chemical properties. Parameter "aa.type" supports following selection: "aaH" (hydrophobicity): Polar(RKEDQN), Neutral(GASTPHY), Hydrophobic(CVLIMFW) "aaV (normalized Van der Waals volume)": Small(GASCTPD), Medium(NVEQIL), Large(MHKFRYW) "aaZ" (polarizability): Low polarizability (GASDT), Medium polarizability (CPNVEQIL), High polarizability(KMHFRYW) "aaP" (polarity): Low polarity (LIFWCMVY), Neutral polarity (PATGS), High polarity (HQRKNED) "aaF": Acidic (DE), Basic (HKR), Polar (CGNQSTY), Nonpolar (AFILMPVW) "aaS": Acidic (DE), Basic (HKR), Aromatic (FWY), Amide (NQ), Small hydroxyl (ST), Sulfur-containing (CM), Aliphatic (AGPILV) "aaE": Acidic (DE), Basic(HKR), Aromatic (FWY), Amide (NQ), Small hydroxyl (ST), Sulfur-containing (CM), Aliphatic 1 (AGP), Aliphatic 2 (ILV)

pwm returns a M*N position weight matrix (PWM) of input sequences. M is the number of elements given by parameter "class". N is the length of each sequence. Each row is a kind of element, and each column is a position. The input sequences must have equal length.

.pathPerl write the path of Perl to perl program file.

.callPerl invoke Perl program via R.

dssp.ss is a vector storing the secondary structure data from DSSP database (http://swift.cmbi.ru.nl/gv/dssp/).

aa.index is a list storing the properties of amino acids from AAIndex database (http://www.genome.jp/aaindex).

PROPERTY is a list sotring the properties of dinucleotide from B-DNA-VIDEO PROPERTY database (http://wwwmgs.bionet.nsc.ru/mgs/systems/bdnavideo/).

DiProDB is a list sotring the conformational and thermodynamic dinucleotide properties from DiProDB database (http://diprodb.fli-leibniz.de/).

Hong Li

  
  ## amino acids groups depend on their hydrophobicity
  aaClass("aaH")
  
  ## load data: dssp.ss
  data(dssp.ss)
  ## see the data in dssp.ss
  dssp.ss[1:5]