u12NbIndex: Extract index of U2 introns (up/down)stream of U12 introns...

View source: R/u12NbIndex.R

u12NbIndexR Documentation

Extract index of U2 introns (up/down)stream of U12 introns rows

Description

Extract row numbers of U2-type introns (up/down)stream of U12-type introns (in the @interestDf attribute of an object of class SummarizedExperiment).

Usage

u12NbIndex(x, intExCol="int_ex", intTypeCol="int_type", 
	strandCol="strand", geneIdCol="collapsed_transcripts", 
	naUnstrand=FALSE)

Arguments

x

Object of type SummarizedExperiment.

intExCol

Column name (or number) that represents whether each row of x assays is "intron" or "exon".

intTypeCol

Column name (or number) that represents what type of intron each row of x assays represents.

strandCol

Column name (or number) that represents the strand of each row of assays in x. The values in the column are either "+", "-" or "*".

geneIdCol

Column name (or number) that represents the gene ID of each row of assays in x.

naUnstrand

Replace unstranded results, i.e. introns or exon with "*" strand, with NA. If set as FALSE (default) "*" strand would be same as "+" strand.

Value

upIntron

A numeric vector which includes the index of U2-type intron upstream the U12-type introns.

downIntron

A numeric vector which includes the index of U2-type intron downstream the U12-type introns.

upExon

A numeric vector which includes the index of exon upstream the U12-type introns.

downExon

A numeric vector which includes the index of exon downstream the U12-type introns.

Author(s)

Ali Oghabian

See Also

u12Index

Examples



head(u12NbIndex(mdsChr22Obj, intExCol="int_ex", 
	intTypeCol="intron_type", strandCol="strand", 
	geneIdCol="collapsed_transcripts_id", naUnstrand=FALSE))
# Return NA if no strand information available
head(u12NbIndex(mdsChr22Obj, intExCol="int_ex", 
	intTypeCol="intron_type", strandCol="strand", 
	geneIdCol="collapsed_transcripts_id", naUnstrand=TRUE))


gacatag/IntEREst documentation built on July 29, 2024, 1:12 a.m.