This function takes a data.table returned by dNdS and sorts the corresponding dNdS value into divergence strata (10-quantile or deciles by default).
divergence_map(dNdS_tbl, subject.id = FALSE, n_quantile = 10)a data.table object returned by dNdS.
a logical value indicating whether query_id AND subject_id should be returned.
a numeric value specifying the number of quantiles that should be returned.
a data.table storing a standard divergence map.
Divergence Strata are typically decile (10-quantile) values of corresponding dNdS values.
The dNdS function returns dNdS values for orthologous genes
of a query species (versus subject species). These dNdS values are then
sorted into deciles and each orthologous protein coding gene of the
query species receives a corresponding decile value instead of the initial dNdS value.
This allows a better comparison between Phylostrata and Divergence Strata (for more details see package: myTAI).
It is also possible to specify other number of quantile (N-quantile) value such as quintile (5-quantile) rather than decile values.
if (FALSE) {
# get a divergence map of example sequences
dNdS_tbl <- 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 )
divMap <- divergence_map( dNdS_tbl )
# in case you want the subject_id as well, you can set
# the argument subject.id = TRUE
divMap <- divergence_map( dNdS_tbl = dNdS_tbl, subject.id = TRUE)
# in case you want a divergence map with divergence stratum as quintile (5-quantile) values
# or any other N-quantile values rather than the default decile (10-quantile) values,
# you can specify this with n_quantile.
divMap <- divergence_map( dNdS_tbl = dNdS_tbl, subject.id = TRUE, n_quantile = 5)
}