addStrandCombination: Add combination of anchor strand orientation.

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

Description

Each anchor region has a strand that is '+' or '-'. Therefore, the each interaction between two regions has one of the following strand combinations: "forward", "reverse", "convergent", or "divergent". Unstranded ranges, indicated by *, are treated as positive strand.

Usage

addStrandCombination(gi, colname = "strandOrientation")

Arguments

gi	GInteractions
colname	name of the new column that is created in gi.

Value

The same GInteractions as gi but with an additional column indicating the four possible combinations of strands "forward", "reverse", "convergent", or "divergent".

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"
)

# add combination of anchor strands as new metadata column
gi <- addStrandCombination(gi)

# build small matrix to check strand combination
cbind(
as.character(strand(anchors(gi, "first"))),
as.character(strand(anchors(gi, "second"))),
mcols(gi)[, "strandOrientation"]
)

ibn-salem/chromloop documentation built on May 18, 2019, 1:29 a.m.