Generating genome summary files for LTRpred.meta results

Source: R/genome.summary.R

Generating genome summary files for LTRpred.meta results

genome.summary(
  genome.folder,
  ltrpred.meta.folder,
  file.name,
  sim = 70,
  cut.range = 2,
  quality.filter = TRUE,
  n.orfs = 0,
  strategy = "default"
)

Arguments

genome.folder

a file path to a folder storing the genome assembly files in fasta format that were used to generate LTRpred annotations of diverse species from the same taxonomic kingdom.
ltrpred.meta.folder

a file path to a folder storing LTRpred annotations of diverse species from the same taxonomic kingdom.
file.name

name of the output file.
sim

LTR similarity threshold. Only putative LTR transposons that fulfill this LTR similarity threshold will be retained.
cut.range

similarity interval size.
quality.filter

shall a quality filter to remove possible false positive predictions be applied?
n.orfs

minimum number of open reading frames a predicted retroelement shall possess.
strategy

quality filter strategy. Options are

  • strategy = "default" : see section Quality Control

  • strategy = "stringent" : in addition to filter criteria specified in section Quality Control, the filter criteria !is.na(protein_domain)) | (dfam_target_name != "unknown") is applied

Details

Generating genome summary files for LTRpred.meta results.

Author

Hajk-Georg Drost