bankSummary {GeneR}R Documentation

Computes informations on all a bank file

Description

This functions computes informations (with function compoSeq, GCcontent, of seqSkew) on a complete bank file.

It returns a data frame with one line by sequences in the bank file.

Parameter "name" can be use to limit the exploration to only a few sequences.

Usage

bankSummary(file, name = NULL, type = "F", fun = compoSeq, seqno = 0)

Arguments

file

Integer/scalar, File name of the bank (fasta file)

seqno

Integer/scalar, Sequence number (buffer number)

name

String/vector, Names of sequences in bank file, NULL: uses all sequences of the bank

type

String/scalar, Bank format ("F" -> fasta. "E" -> embl, "G" -> GenBank)

fun

Function, Function to be used (for example seqSkew

Value

a data frame with one line by sequence.

Author(s)

Antoine Lucas

See Also

bankDensityProfile

Examples

  for(i in 1:8)
  {
    s=randomSeq(n=100)
    placeString(s,seqno=0)
    writeFasta("toto_norm.fa",append=TRUE,name=i)
  }
  bankSummary(file="toto_norm.fa")
  bankSummary(file="toto_norm.fa",fun=seqSkew)

[Package GeneR version 2.24.0 Index]