u12NbIndex {IntEREst} | R Documentation |
Extract row numbers of U2-type introns (up/down)stream of U12-type introns (in
the @interestDf
attribute of an object of class
SummarizedExperiment
).
u12NbIndex(x, intExCol="int_ex", intTypeCol="int_type", strandCol="strand", geneIdCol="collapsed_transcripts", naUnstrand=FALSE)
x |
Object of type |
intExCol |
Column name (or number) that represents whether each row of |
intTypeCol |
Column name (or number) that represents what type of intron each row of
|
strandCol |
Column name (or number) that represents the strand of each row of assays in
|
geneIdCol |
Column name (or number) that represents the gene ID of each row of assays in
|
naUnstrand |
Replace unstranded results, i.e. introns or exon with "*" strand, with NA. If set as FALSE (default) "*" strand would be same as "+" strand. |
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. |
Ali Oghabian
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))