rebuildStrandModel: Rebuild a Strand Model

In hyf97ca/hotgenes: Simulates Heat Physics on your RNA-seq Dataset for More Compelling Visualization

Description

This function is cheaper than rebuilding a brand new strand model from scratch. These savings are realized by using parts of the old strand model.

Usage

rebuildStrandModel(strandModel, newStartBase, newEndBase, newScaling,
  startBase, endBase, scaling)

Arguments

strandModel	a strand model that is a superset of the new strand model with tighter scaling
newStartBase	an integer depicting the desired start base pair number.
newEndBase	an integer depicting the desired end base pair number.
newScaling	scaling factor in how many base pairs should be represented per index. Should be larger (eg. 1000000) than old scaling factor. IMPORTANT: newScaling is assumed to be divisible by scaling.
startBase	an integer depicting the old strand model's starting base pair number. Should be the beginning of the chromosome to be rendered (eg. 1).
endBase	an integer depicting the old strand model's starting base pair number. Should be the end of the chromosome to be rendered (eg. 3000000).
scaling	scaling factor in how many base pairs should be represented per index in the existing strand model. Should be smaller than any rebuilt choice (eg. 1)

Value

a strand model with the new start-end base and/or more relaxed scaling

Examples

## Not run: 
   sm <- generateStrandModel(startBase=1, endBase=195471971,
    fc=musCh1fc, chr="chr1", strand="-", scaling=1)
   sm1 <- rebuildStrandModel(strandModel=sm, newStartBase=1000,
    newEndBase=2000, newScaling=100000, startBase=1, endBase=195471971, scaling=1)

## End(Not run)

hyf97ca/hotgenes documentation built on Dec. 8, 2019, 12:41 p.m.