u12NbIndex {IntEREst} | R 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))

[Package IntEREst version 1.4.1 Index]