addMSA: Add MSA to scores matrix (for developers)

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

Add MSA to scores matrix (for developers)

Description

Meant for developers only.

Usage

addMSA(ref_col2res, alt_col2res, hit_mat)

Arguments

ref_col2res	output of recodeMSA for base MSA
alt_col2res	output of recodeMSA for alternative MSA
hit_mat	output of initCounter for base MSA Cmatrix (recodeMSA)

Details

Based on the output of recodeMSA and initCounter the MSAs are compared and scores are added to the scores matrix (initCounter matrix)

Author(s)

Franz-Sebastian Krah

Examples

## Not run: 
## Minimal (unrealistic) example for the score computation
# Base MSA
s <- matrix(c("-", "a", "c", "t", "g", 
"-", "a", "c", "t", "g", 
"a", "-", "c", "t", "g"), 3,5, byrow = T)
s <- as.DNAbin(s)

# Alternative MSA
s.alt <- matrix(c("-", "a", "c", "t", "g", "-", 
"a", "c", "t", "g", "-", 
"a", "c", "t", "g"), 3,5, byrow = T)
s.alt <- as.DNAbin(s.alt)

# Recode base MSA (Cmatrix)
s.recode <- recodeMSA(msa = s)

# Recode alt MSA (Cmatrix)
s.alt.recode <- recodeMSA(msa = s.alt)

# Initialize counter (basis for residue pair score)
s.counter <- initCounter(s.recode)
s.counter
# Update counter
s.counter <- addMSA(ref_col2res = s.recode, alt_col2res = s.alt.recode, hit_mat = s.counter)

## End(Not run)

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