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Filter dNdS values

Source: R/filter_dNdS.R
filter_dNdS.Rd

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

Usage

filter_dNdS(dNdS_tbl, dnds.threshold = 2)

Arguments

dNdS_tbl

a data.table returned by dNdS.

dnds.threshold

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.

Details

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.

See also

dNdS, divergence_stratigraphy

Author

Hajk-Georg Drost

Examples

if (FALSE) { # \dontrun{

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)
                  
} # }