Starr (version 1.28.0)

filterGenes: Filter Features/Genes

Description

This fucntion filters genes and other annotated features with respect to length, ovelaps and distance to other features.

Usage

filterGenes(gffAnno, distance_us=500, distance_ds=500, minLength=-Inf, maxLength=Inf)

Arguments

gffAnno

a data frame containing the annotation

distance_us

how many basepairs upstream to the feature should not overlap with other features.

distance_ds

how many basepairs downstream to the feature should not overlap with other features.

minLength

minimal length of the feature

maxLength

maximal length of the feature

Value

a character vector with the names of the features, that passed the filter.

Examples

##
# dataPath <- system.file("extdata", package="Starr")
# transcriptAnno <- read.gffAnno(file.path(dataPath, "transcriptAnno.gff"), feature="transcript")
# filtered_transcripts <- filterGenes(transcriptAnno, distance_us = 0, distance_ds = 0, minLength = 1000)