filterGenes: Filter Features/Genes

In Starr: Simple tiling array analysis of Affymetrix ChIP-chip data

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.

Author(s)

Benedikt Zacher [e-mail]

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)

Starr documentation built on April 28, 2020, 7:52 p.m.