initCounter: Initialize counters matrix (for developers)

In FranzKrah/rGUIDANCE: rGUIDANCE – alignment confidence score computation in R

Initialize counters matrix (for developers)

Description

Meant for developers only.

Usage

initCounter(col2res)

Arguments

col2res

Output from recodeMSA

Details

Produce res_pair_hit object as basis for comparing residue pairs. This matrix contains all residue pairs in the MSA and the information if they are bases (hit = 0) or gabs (-1); the hits are later updated by comparisons with the alternative MSAs (see add_msa). The function 'init_counters' in 'set_msa_score' (see recodeMSA) uses 3D matrices, which is not straight forewardly implemented in Rcpp, which is why I work with a nxk matrix, with k many columns as the REF MSA and n rows for all residue pairs. This is almost equally fast, however, the subsequent calculation of derived scores is not as handy. These are done in the function 'scores'.

For an example see addMSA

Author(s)

Franz-Sebastian Krah

FranzKrah/rGUIDANCE documentation built on Jan. 27, 2024, 10:42 a.m.