applyOverlap {IntEREst} | R Documentation |
Runs a function on columns of the counts (assay) of a 'SummarizedExperiment'
object (resulted by interest()
, interest.sequential()
or
readInterestResults()
) based on the overalp of its exon/intron
coordinates with those of another 'SummarizedExperiment' object. The number of
the rows and the dimensions of the counts of the result are equal to those of
the subject
. The function is applied on the query based on it's overlap
to the subject.
applyOverlap( query, subject, type="any", replaceValues=FALSE, intExCol="int_ex", intronExon="intron", sujectGeneNamesCol, repeatsTableToFilter=c(), scaleFragment=TRUE, scaleLength=TRUE, unmapValue=0, FUN=mean, ... )
query, subject |
SummarizedExperiment objects resulted by |
type |
The type of overlap. By default it considers any overlap. See findOverlaps for more info. |
replaceValues |
Whether return a 'SummarizedExperiment' object with new counts (resulted by running function) replaced. |
intExCol |
Column name (or number) in the rowData of the objects that represents whether each row of the assay is "intron" or "exon". |
intronExon |
Should be assigned either |
sujectGeneNamesCol |
The column in the row data of the subject that includes the gene names. |
repeatsTableToFilter |
A data.frame table that includes chr,begin and end columns. If defined, all reads mapped to the described regions will be ingnored. |
scaleFragment |
Logical value, indicating whether the retention levels must be scaled by (genewide) fragment levels. |
scaleLength |
Logical value, indicating whether the retention levels must be scaled by length of the introns/exons. |
unmapValue |
The value to assign to unmapped rows (i.e. introns/exons). |
FUN |
The function to apply. |
... |
Other parameter settings from |
The returned value is a data frame if replaceValues
is FALSE and it is
SummarizedExperiment if replaceValues
is TRUE.
Ali Oghabian
readInterestResults
interest
interest.sequential
mdsChr22Obj tmp<- applyOverlap( query=mdsChr22Obj, subject=mdsChr22Obj, type="equal", replaceValues=FALSE, intExCol="int_ex", intronExon="intron", sujectGeneNamesCol="collapsed_transcripts", scaleFragment=TRUE, scaleLength=TRUE, unmapValue=0, FUN=head, n=1 )