packsToCsv: Save packFinder Results in CSV Format (.csv)

In jackgisby/packFinder: de novo Annotation of Pack-TYPE Transposable Elements

Save packFinder Results in CSV Format (.csv)

Description

Saves a dataframe of potential Pack-TYPE elements, usually generated via packSearch. May be retrieved using getPacksFromCsv.

Usage

packsToCsv(packMatches, file)

Arguments

packMatches

A dataframe containing genomic ranges and names referring to sequences to be extracted. Can be obtained from packSearch or generated from a GRanges object, after conversion to a dataframe. Must contain the following features: start - the predicted element's start base sequence position. end - the predicted element's end base sequence position. seqnames - character string referring to the sequence name in Genome to which start and end refer to.

file

CSV file save path.

Value

Save location of csv file.

Author(s)

Jack Gisby

See Also

getPacksFromCsv, write.table, packSearch

Examples

data(packMatches)

packsToCsv(
    packMatches, 
    system.file("extdata", "packMatches.csv", package = "packFinder")
)

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