applyOverlap: Apply function over counts

Description Usage Arguments Value Author(s) See Also Examples

View source: R/applyOverlap.R

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

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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

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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
)

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