addInteractionSupport: Add column to 'GInteractions' with overlap support.

In ibn-salem/sevenC: Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs

Description

See overlap methods in InteractionSet package for more details on the overlap calculations: ?overlapsAny

Usage

addInteractionSupport(gi, subject, colname = "loop", ...)

Arguments

gi	GInteractions object
subject	another GInteractions object
colname	name of the new annotation column in gi.
...	additional arguments passed to overlapsAny.

Value

InteractionSet gi as input but with additional annotation column colname indicating whether each interaction is supported by subject or not.

Examples

# build example GRanges as anchors
anchorGR <- GRanges(
 rep("chr1", 4),
 IRanges(
   c(1, 5, 20, 14),
   c(4, 8, 23, 17)
 ),
 strand = c("+", "+", "+", "-"),
 score = c(5, 4, 6, 7)
)


# build example GIntreaction object
gi <- GInteractions(
 c(1, 2, 2),
 c(4, 3, 4),
 anchorGR,
 mode = "strict"
)

# build exapple support GInteractions object
exampleSupport <- GInteractions(
    GRanges("chr1", IRanges(1, 4)),
    GRanges("chr1", IRanges(15, 20))
)

# add support
gi <- addInteractionSupport(gi, subject = exampleSupport)

# Use colname argument to add support to differnt metadata column name
gi <- addInteractionSupport(gi, subject = exampleSupport, colname = "example")

ibn-salem/sevenC documentation built on May 17, 2019, 11:16 p.m.