virtual 4C

[robinweide]

Base this on the new APA-function

[robinweide]

update: main function works, visualise not: 7fac99c

[robinweide]

visualise.virtual4C_discovery now works 7cd990b

I still need to:

• streamline both
• enable list of exps

[robinweide]

392042b :
made everything neater and added man-entries

[robinweide]

This is the current stage:

• anchor
• option to add bed underneath (here: loop anchors called with HICCUPS)

[robinweide]

someday:

• multiple Hi-C (both as input for virtual_4C and as bundle for vis)
• multiple beds in vis

[teunbrand]

You can now have multiple viewpoints in visualisation when bundling experiments. Also, multiple beds are an option.

bed1 <- data.frame("chr1", c(25e6, 125e6), c(50e6, 150e6))
bed2 <- data.frame("chr1", 75e6, 100e6)
bedlist <- list(bed1, bed2)

v4c1 <- virtual_4C(exp, data.frame("chr1", 25e6, 30e6))
v4c2 <- virtual_4C(exp, data.frame("chr1", 75e6, 80e6))

v4c <- bundle(v4c1, v4c2)

visualise(v4c, bedlist = bedlist, 
          bed_colours = c("dodgerblue", "limegreen"))

[teunbrand]

Closing this, as it is now able to do multiple experiments, multiple viewpoints can be bundles and multiple beds can be visualised.