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Recode an RVD alignment as similarity to a reference row

Source: R/tales_plot.R
dot-rvd_to_match_align.Rd

Substitutes each RVD with a score expressing how similar its DNA-binding preference is to the RVD of a reference TALE, column by column. This is the RVD-level counterpart of .domain_to_sim_align(), which works on protein sequence similarity instead: the two come apart, since domains can be sequence-divergent yet share an RVD, or near-identical yet differ at positions 12-13.

Usage

.rvd_to_match_align(rvd_align, rvd_sims = rvdSimDf, ref_tag = NULL)

Arguments

rvd_align

A character matrix of aligned RVDs.

rvd_sims

A data frame of pairwise RVD similarity with columns rvd1, rvd2 and Cor. Defaults to the package's internal rvdSimDf.

ref_tag

Pattern selecting the reference row; see .pick_ref_name().

Value

A numeric matrix with the dimensions and dimnames of rvd_align.

Details

Wired through fill_type = "rvd_sim" in plot.tales_msa – the RVD-level counterpart of "domain_sim". The internal rvdSimDf dataset it reads also feeds .rvd_score_table().