filterWildcards: Remove Low Quality Sequences
In jackgisby/packFinder: de novo Annotation of Pack-TYPE Transposable Elements

filterWildcards

R Documentation

Remove Low Quality Sequences

Description

Takes transposable elements detected by packSearch and removes those with large numbers of wildcard ("N") bases. Used by packClust and packAlign to remove poor quality sequences that may interfere with the quality of sequence alignments.

Usage

filterWildcards(packMatches, Genome, maxWildcards = 0.05)

Arguments

`packMatches`	A dataframe containing genomic ranges and names referring to sequences to be extracted.
`Genome`	The original set of sequences used to generate the transposons detected by `packSearch`.
`maxWildcards`	The maximal allowable proportion of wildcards in the sequence of each match (defaults to `0.05`).

Value

The original dataframe, packMatches, with sequences removed that are found to contain a proportion of wildcards ("N") greater than that specified in maxWildcards.

Author(s)

Jack Gisby

Examples

data(arabidopsisThalianaRefseq)
data(packMatches)
    
filteredMatches <- filterWildcards(
    packMatches, 
    arabidopsisThalianaRefseq, 
    maxWildcards = 0.05
)

jackgisby/packFinder documentation built on July 19, 2022, 2:25 a.m.