bankSummary {GeneR} | R Documentation |
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.
bankSummary(file, name = NULL, type = "F", fun = compoSeq, seqno = 0)
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 |
a data frame with one line by sequence.
Antoine Lucas
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)