Subset linkSet object based on bait names

Subset linkSet object based on bait names

Subset linkSet object based on bait regions

Subset linkSet object based on other end (oe) regions

Usage

# S4 method for class 'linkSet'
subsetBait(x, subset)

# S4 method for class 'linkSet'
subsetBaitRegion(x, subset)

# S4 method for class 'linkSet'
subsetOE(x, subset)

Arguments

x

A linkSet object

subset

A GRanges object specifying the regions to keep

Value

A new linkSet object containing only the specified bait interactions

A new linkSet object containing only the interactions with bait regions overlapping the subset

A new linkSet object containing only the interactions with oe regions overlapping the subset

Examples

data(linkExample)
subset_bait_names <- c("bait1", "bait2")
subsetted_linkSet <- subsetBait(linkExample, subset_bait_names)
data(linkExample)
subset_bait_regions <- GRanges(seqnames = "chr1", ranges = IRanges(start = c(100, 200), end = c(150, 250)))
subsetted_linkSet <- subsetBaitRegion(linkExample, subset_bait_regions)
data(linkExample)
subset_oe_regions <- GRanges(seqnames = "chr1", ranges = IRanges(start = c(300, 400), end = c(350, 450)))
subsetted_linkSet <- subsetOE(linkExample, subset_oe_regions)