getFlags: Flag regions with genomic events of interest

In leekgroup/derfinder: Differential expression analysis of RNA-seq data at base-pair resolution

Description

Connects results of tornado pipeline to existing annotation as a way to determine which regions may point to interesting biological events.

Usage

getFlags(regions, exons, chromosome, pctcut = 0.8)

Arguments

regions	data frame of regions to consider, usually the $states output of getRegions
exons	data frame containing annotated exons you would like to consider. Should have columns chr,start,end,exon_id, and gene. Can be created with getAnnotation.
chromosome	Chromosome you're considering. Currently you can only do one chromosome at a time.
pctcut	What percentage of an exon should a region overlap in order to call that exon differentially expressed? Default 0.8 (meaning 80%).

Value

List with elements having length equal to the number of rows in regions:

flags	Event indicated by corresponding region
flag.info	Genomic features (exons) associated with genomic events
percent.exon	The percent of the exon (in flag.info) overlapped by this region

Author(s)

Alyssa Frazee

See Also

getAnnotation

leekgroup/derfinder documentation built on May 20, 2019, 11:30 p.m.