Classify TRD genes as derived from either DNA transposons or retrotransposons

Usage

get_transposed_classes(pairs, intron_counts)

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_transposed().
intron_counts: A 2-column data frame with columns gene and introns indicating the number of introns for each gene, as returned by get_intron_counts.

Value

A 3-column data frame with the following 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), "dTRD" (DNA transposon-derived duplication), "rTRD" (retrotransposon-derived duplication), and "DD" (dispersed duplication).

Examples

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

# Get processed annotation
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
annotation <- pdata$annotation

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

# Classify pairs
trd <- get_transposed(pairs, diamond_inter, annotation)

# Create TxDb object from GRanges
library(txdbmaker)
txdb <- txdbmaker::makeTxDbFromGRanges(yeast_annot[[1]])
#> 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.factor()' 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.factor()' 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.factor()' 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.factor()' is deprecated.  Use 'as.data.frame.vector()' or 'as.data.frame()' instead

# Get intron counts
intron_counts <- get_intron_counts(txdb)

# Get TRD classes
trd_classes <- get_transposed_classes(trd, intron_counts)