View source: R/quality.filter.meta.R
quality.filter.meta | R Documentation |
This function takes the file paths to the genomes folder and LTRpred.meta
output folder as input and eliminates false positive retrotransposon predictions on a metagenomic scale.
quality.filter.meta( kingdom, genome.folder, ltrpred.meta.folder, sim, cut.range = 2, n.orfs, strategy, update = FALSE )
kingdom |
a character string specifying the kingdom of life to which genomes annotated with |
genome.folder |
path to folder storing the genome assembly files that were used for |
ltrpred.meta.folder |
path to folder storing the |
sim |
LTR similarity threshold. Only putative LTR transposons that fulfill this LTR similarity threshold will be retained. |
cut.range |
a numeric number indicating the interval size for binning LTR similarities. |
n.orfs |
minimum number of ORFs detected in the putative LTR transposon. |
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
LTRpred
, LTRpred.meta
, read.ltrpred
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