extractRegion: Extract a subset of the HTCexp object

In bioinfo-pf-curie/HiTC: High Throughput Chromosome Conformation Capture analysis

Description

Extract a subset of the HTCexp object based on genomic ranges

Usage

extractRegion(x, MARGIN, chr, from, to, exact=FALSE)

Arguments

x	object that inherits from class HTCexp
MARGIN	a vector giving the subscripts which the function will be applied over as in 'apply' function. E.g., '1' for the 'x' intervals, and '2' for the 'y' intervals, 'c(1, 2)' indicates 'x' and 'y' intervals.
chr	character; the chromosome of the genomic region
from	numeric; start of the genomic region
to	numeric; end of the genomic region
exact	logical; exact genomic region

Details

By default, only the intervals fully included in the genomic ranges are returned. If exact is true, the overlapping intervals are also used, and forced to start/end at the specified position. If no intervals are overlapping, an interval with NA values is added.

Value

A HTCexp object

Author(s)

N. Servant

See Also

GRanges-class

Examples

data(Nora_5C)

## Focus on the genomic region chrX:98000000-100000000
E14sub<-extractRegion(E14$chrXchrX, c(1,2), chr="chrX", from=98000000, to=100000000)
show(E14sub)

bioinfo-pf-curie/HiTC documentation built on May 17, 2019, 6:39 p.m.