Calculate Ka, Ks, and Ka/Ks from duplicate gene pairs

Usage

pairs2kaks(
  gene_pairs_list,
  cds,
  model = "MYN",
  bp_param = BiocParallel::SerialParam()
)

Arguments

gene_pairs_list: List of data frames containing duplicated gene pairs as returned by classify_gene_pairs().
cds: List of DNAStringSet objects containing the coding sequences of each gene.
model: Character scalar indicating which codon model to use. Possible values are "Li", "NG86", "NG", "LWL", "LPB", "MLWL", "MLPB", "GY", "YN", "MYN", "MS", "MA", "GNG", "GLWL", "GLPB", "GMLWL", "GMLPB", "GYN", and "GMYN". Default: "MYN".
bp_param: BiocParallel back-end to be used. Default: BiocParallel::SerialParam().

Value

A list of data frames containing gene pairs and their Ka, Ks, and Ka/Ks values.

Examples

data(diamond_intra)
data(diamond_inter)
data(yeast_annot)
data(yeast_seq)
data(cds_scerevisiae)
blast_list <- diamond_intra
blast_inter <- diamond_inter

pdata <- syntenet::process_input(yeast_seq, yeast_annot)
#> Warning: Direct call of 'as.data.frame.factor()' is deprecated.  Use 'as.data.frame.vector()' or 'as.data.frame()' instead
#> Warning: Direct call of 'as.data.frame.integer()' is deprecated.  Use 'as.data.frame.vector()' or 'as.data.frame()' instead
#> Warning: Direct call of 'as.data.frame.factor()' is deprecated.  Use 'as.data.frame.vector()' or 'as.data.frame()' instead
#> Warning: Direct call of 'as.data.frame.integer()' is deprecated.  Use 'as.data.frame.vector()' or 'as.data.frame()' instead
annot <- pdata$annotation["Scerevisiae"]

# Binary classification scheme
pairs <- classify_gene_pairs(annot, blast_list)
td_pairs <- pairs[[1]][pairs[[1]]$type == "TD", ]
gene_pairs_list <- list(
    Scerevisiae = td_pairs[seq(1, 3, by = 1), ]
)

cds <- list(Scerevisiae = cds_scerevisiae)

kaks <- pairs2kaks(gene_pairs_list, cds)