This function takes the output data.table returned by dNdS and
filters the output by the following criteria:
1) all dN values having an NA value are omitted
2) all dS values having an NA value are omitted
3) all dNdS values >= the specified dnds.threshold are omitted
filter_dNdS(dNdS_tbl, dnds.threshold = 2)a data.table returned by dNdS.
a numeric value specifying the dnds threshold for genes that shall be retained.
Hence all genes having a dNdS value <= dnds.threshold are retained. Default is dnds.threshold = 2.
The dNdS ratio quantifies the selection pressure acting on a given protein sequence.
It is proposed that:
1) dNdS values < 1 reflect stabilizing selection of a protein
2) dNdS value = 1 reflect neutral selection of a protein
3) dNdS values > 1 reflect variational selection of a protein
Now an assumption must be generated to allow for dNdS filtering.
Given a dnds.threshold all value above this threshold are omitted from the dataset.
if (FALSE) {
filter_dNdS( dNdS( query_file =
system.file('seqs/ortho_thal_cds.fasta', package = 'orthologr'),
subject_file =
system.file('seqs/ortho_lyra_cds.fasta', package = 'orthologr'),
ortho_detection = "RBH",
aa_aln_type = "pairwise",
aa_aln_tool = "NW",
codon_aln_tool = "pal2nal",
dnds_est.method = "Comeron",
comp_cores = 1),
dnds.threshold = 2)
# a small example using clustalw
filter_dNdS( dNdS( query_file =
system.file('seqs/ortho_thal_cds.fasta', package = 'orthologr'),
subject_file =
system.file('seqs/ortho_lyra_cds.fasta', package = 'orthologr'),
ortho_detection = "RBH",
aa_aln_type = "pairwise",
aa_aln_tool = "NW",
codon_aln_tool = "pal2nal",
dnds_est.method = "Comeron",
comp_cores = 1) ,
dnds.threshold = 2)
}