genome.summary: Generating genome summary files for 'LTRpred.meta' results

In HajkD/LTRpred: De novo functional annotation of retrotransposons

Generating genome summary files for LTRpred.meta results

Description

Generating genome summary files for LTRpred.meta results

Usage

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(s)

Hajk-Georg Drost

HajkD/LTRpred documentation built on April 22, 2022, 4:35 p.m.