MD.plot2: Visualize the MD plot.

In dozmorovlab/HiCdiff: HiCdiff: Joint normalization and comparative analysis of multiple Hi-C datasets

Description

Visualize the MD plot.

Usage

MD.plot2(M, D, p.val = NA, diff.thresh = NA)

Arguments

M	The M component of the MD plot. Available from the hic.table object.
D	The D component of the MD plot. The unit distance of the interaction. Available from the hic.table object.
p.val	An optional p-value vector to provide color to the plot based on the significance of the differences between the IFs.
diff.thresh	A difference threshold used for calculating p-values. If set to a value will add dotted horizontal lines to the plot to display the threshold cutoffs. See 'hic_loess' or 'hic_diff' functions help for more information on this parameter.

Value

An MD plot.

Examples

data('HMEC.chr22')
data('NHEK.chr22')
hic.table <- create.hic.table(HMEC.chr22, NHEK.chr22, chr='chr22')
# Plug hic.table into hic_loess()
result <- hic_loess(hic.table)
# perform difference detection
diff.result <- hic_diff(result, diff.thresh = 1)
MD.plot2(diff.result$M, diff.result$D, diff.result$p.value)

dozmorovlab/HiCdiff documentation built on May 20, 2019, 11:13 a.m.