Classify gene pairs derived from tandem and proximal duplications

Usage

get_tandem_proximal(pairs = NULL, annotation_granges = NULL, proximal_max = 10)

Arguments

pairs: A 3-column data frame with columns dup1, dup2, and type indicating duplicated gene 1, duplicated gene 2, and the mode of duplication associated with the pair. This data frame is returned by get_segmental().
annotation_granges: A processed GRanges object as in each element of the list returned by syntenet::process_input().
proximal_max: Numeric scalar with the maximum distance (in number of genes) between two genes to consider them as proximal duplicates. Default: 10.

Value

A 3-column data frame with the variables:

dup1: Character, duplicated gene 1.
dup2: Character, duplicated gene 2.
type: Factor of duplication types, with levels "SD" (segmental duplication), "TD" (tandem duplication), "PD" (proximal duplication), and "DD" (dispersed duplication).

Examples

data(yeast_annot)
data(yeast_seq)
data(fungi_kaks)
scerevisiae_kaks <- fungi_kaks$saccharomyces_cerevisiae

# Get processed annotation for S. cerevisiae
pdata <- annotation <- 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[[1]]

# Get duplicated pairs
pairs <- scerevisiae_kaks[, c("dup1", "dup2", "type")]
pairs$dup1 <- paste0("Sce_", pairs$dup1)
pairs$dup2 <- paste0("Sce_", pairs$dup2)

# Get tandem and proximal duplicates
td_pd_pairs <- get_tandem_proximal(pairs, annot)