applyOverlap: Apply function over counts

In gacatag/IntEREst: Intron-Exon Retention Estimator

Apply function over counts

Description

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.

Usage

applyOverlap(
	query,
	subject,
	type="any",
	replaceValues=FALSE,
	intExCol="int_ex", 
	intronExon="intron",
	sujectGeneNamesCol,
	repeatsTableToFilter=c(),
	scaleFragment=TRUE,
	scaleLength=TRUE,
	unmapValue=0,
	FUN=mean,
	...
)

Arguments

query, subject	SummarizedExperiment objects resulted by interest(), interest.sequential() or readInterestResults() functions.
type	The type of overlap. By default it considers any overlap. See findOverlaps-methods 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 'intron' or 'exon' or c('intron','exon') based on whether match the PWM to the intronic, exonic, or intronic and exonic regions of the reference. By default it seeks matches in intronic regions (intronExon='intron').
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 aggregate() function.

Value

The returned value is a data frame if replaceValues is FALSE and it is SummarizedExperiment if replaceValues is TRUE.

Author(s)

Ali Oghabian

See Also

readInterestResults interest interest.sequential

Examples

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
)

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