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

In IntEREst: Intron-Exon Retention Estimator

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))

IntEREst documentation built on Nov. 8, 2020, 8:05 p.m.