Classify gene pairs originating from transposon-derived duplications

Usage

get_transposed(
  pairs,
  blast_inter,
  annotation,
  evalue = 1e-10,
  anchors = 5,
  max_gaps = 25,
  collinearity_dir = NULL
)

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_tandem_proximal().
blast_inter: A list of data frames of length 1 containing BLAST tabular output for the comparison between the target species and an outgroup. Names of list elements must match the names of list elements in annotation. BLASTp, DIAMOND or simular programs must be run on processed sequence data as returned by syntenet::process_input().
annotation: A processed GRangesList or CompressedGRangesList object as returned by syntenet::process_input().
evalue: Numeric scalar indicating the E-value threshold. Default: 1e-10.
anchors: Numeric indicating the minimum required number of genes to call a syntenic block, as in syntenet::infer_syntenet. Default: 5.
max_gaps: Numeric indicating the number of upstream and downstream genes to search for anchors, as in syntenet::infer_syntenet. Default: 25.
collinearity_dir: Character indicating the path to the directory where .collinearity files will be stored. If NULL, files will be stored in a subdirectory of tempdir(). Default: NULL.

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), "TRD" (transposon-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)