FindHighlyExpressedGenes: Find Highly Expressed Genes

In fredysiegrist/statanacoseq: Statistical Analyses of Codon Usage in Custom Genome Sequences

Description

FindHighlyExpressedGenes Finds Highly Expressed Genes in Lost

Usage

FindHighlyExpressedGenes(n = 100, tag = "PROTEXPR")

Arguments

n	Integer
tag	String either 'PROTEXPR' or 'MRNAEXPR'

Details

Should work the same as FindHighlyExpressedGenes() in Darwin on DB

Value

VOID

Original code in Darwin

Compute CAI, the Codon Adaptation Index (Sharp and Li 1987)

FindHighlyExpressedGenes := proc( ; n=100:integer, tag='PROTEXPR':string)
 # tags: 'PROTEXPR' 'MRNAEXPR'
 expr := CreateArray(1..DB[TotEntries]);
 for i to DB[TotEntries] do
   ex := sscanf(SearchTag(tag, Entry(i)), '
   if ex <> [] then
     expr[i] := op(ex) fi;
 od;
 sorted := sort(expr);
 limit := sorted[length(sorted)-n+1];
 genes := [];
 for i to DB[TotEntries] do
   if expr[i] >= limit then
     genes := append(genes, i) fi od;
   genes
end: 

Author(s)

Roth, A.; Friberg, M.; Siegrist, F. and Cannarozzi, G. M. [e-mail]

See Also

seqinr statanacoseq CodonProbabilities

Examples

FindHighlyExpressedGenes()

fredysiegrist/statanacoseq documentation built on May 16, 2019, 2:44 p.m.