dev/DEV-scores.R

In heibl/polenta: Multiple Sequence Alignment with PASTA and GUIDANCE

load("dev/scores.rda")
names(scores)



head(scores$column_score)

id <- scores$residue_pair_column_score$col %in% scores$column_score$col
id <-  scores$column_score$col %in% scores$residue_pair_column_score$col

cs <- scores$column_score


x <- cbind(cs$CS[rpcs$col], rpcs$col_score)


sapply(scores, dim)
head(rprs)

## residue_pair_residue_score as matrix
rprs <- scores$residue_pair_residue_score
m <- matrix(rprs$score, nrow = nrow(base.msa))
identical(dim(base.msa), dim(m)) # alignment and rprs matrix have same dimensions

x <- polentaDNA(base.msa, m)

## calculate residue_pair_column_score from m
rpcs <- colMeans(m, na.rm = TRUE)
rpcs <- rpcs[!is.na(rpcs)]
# id <- which(rpcs != scores$residue_pair_column_score$col_score)
# cbind(rpcs, scores$residue_pair_column_score$col_score)[id, ]

## calculate residue_pair_sequence_score from m
rpss <- rowMeans(m, na.rm = TRUE)
rpss <- rpss[!is.na(rpss)]
# id <- which(rpcs != scores$residue_pair_column_score$col_score)
# cbind(rpcs, scores$residue_pair_column_score$col_score)[id, ]