est_optimal_codons
and get_fop
now work
on codon frequency matrix like other cubar functions.
codon optimization can be done at both family(amino acid) or
subfamily level now and optimal codons can be estimated for each level
using either codon bias or gene expression levels (Thanks @maltesemike for
valuable suggestions and feedback). The false discovery rate is
controlled by the fdr
argument.
There were two RSCU columns (RSCU
and
rscu
) in the output of est_optimal_codons
and
get_fop
. Now only rscu
is kept and represents
the RSCU values.
New functions to perform sliding window analysis on codon usage:
slide
, slide_codon
, slide_apply
and slide_plot
.
New function to calculate the deviation from proportionality (Dp)
of host tRNA availability: get_dp
.
codon_optimize
&
codon_diff
)get_cscg
that caused an error when the
input codon frequency matrix has a single row.est_trna_weight
. Now zero w values were
replaced with geometric mean (rather than the arithmetic mean) of
non-zero w values.est_optimal_codons
.data.table
reference semantics.get_enc
codeget_enc
for non-standard genetic
code.