edit_order: Edit sequence ordered by reference genome positions comparing...

In mmollina/MAPPoly: Genetic Linkage Maps in Autopolyploids

Edit sequence ordered by reference genome positions comparing to another set order

Description

Edit sequence ordered by reference genome positions comparing to another set order

Usage

edit_order(input.seq, invert = NULL, remove = NULL)

Arguments

input.seq	object of class mappoly.sequence with alternative order (not genomic order)
invert	vector of marker names to be inverted
remove	vector of marker names to be removed

Value

object of class mappoly.edit.order: a list containing vector of marker names ordered according to editions ('edited_order'); vector of removed markers names ('removed'); vector of inverted markers names ('inverted').

Author(s)

Cristiane Taniguti, [e-mail]

Examples

 
  dat <- filter_segregation(tetra.solcap, inter = FALSE)
  seq_dat <- make_seq_mappoly(dat)
  seq_chr <- make_seq_mappoly(seq_dat, arg = seq_dat$seq.mrk.names[which(seq_dat$chrom=="1")])

  tpt <- est_pairwise_rf(seq_chr)
  seq.filt <- rf_snp_filter(tpt, probs = c(0.05, 0.95))
  mat <- rf_list_to_matrix(tpt)
  mat2 <- make_mat_mappoly(mat, seq.filt)

  seq_test_mds <- mds_mappoly(mat2)
  seq_mds <- make_seq_mappoly(seq_test_mds)
  edit_seq <- edit_order(input.seq = seq_mds)
 
 

mmollina/MAPPoly documentation built on June 10, 2025, 10:20 p.m.