View source: R/generate.multi.quality.filter.meta.R
generate.multi.quality.filter.meta | R Documentation |
quality.filter.meta
for several different ltr similarity thresholds.A helper function to apply the quality.filter
function to diverse LTRpred
annotations while probing different ltr similarity thresholds.
generate.multi.quality.filter.meta( kingdom, genome.folder, ltrpred.meta.folder, sim.options, cut.range.options, n.orfs = 0, strategy = "default", update = FALSE )
kingdom |
the taxonomic kingdom of the species for which |
genome.folder |
a file path to a folder storing the genome assembly files in fasta format that
were used to generate |
ltrpred.meta.folder |
a file path to a folder storing |
sim.options |
a numeric vector storing the ltr similarity thresholds that shall be probed. |
cut.range.options |
a numeric vector storing the similarity cut range thresholds that shall be probed. |
n.orfs |
minimum number of open reading frames a predicted retroelement shall possess. |
strategy |
quality filter strategy. Options are
|
update |
shall already existing |
Quality Control
ltr.similarity
: Minimum similarity between LTRs. All TEs not matching this
criteria are discarded.
n.orfs
: minimum number of Open Reading Frames that must be found between the
LTRs. All TEs not matching this criteria are discarded.
PBS or Protein Match
: elements must either have a predicted Primer Binding
Site or a protein match of at least one protein (Gag, Pol, Rve, ...) between their LTRs. All TEs not matching this criteria are discarded.
The relative number of N's (= nucleotide not known) in TE <= 0.1. The relative number of N's is computed as follows: absolute number of N's in TE / width of TE.
A list with to list elements sim_file
and gm_file
. Each list element stores a data.frame
:
sim_file
(similarity file)
This data.frame
stores the information
gm_file
(genome metrics file)
This data.frame
stores the information
Hajk-Georg Drost
quality.filter
, quality.filter.meta
, LTRpred
, LTRpred.meta
, read.ltrpred
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