clusterdef.ncopies: clusterdef.ncopies
In chr1swallace/caller: caller

Description Usage Arguments Details Value Author(s)

Create a clusterdef object, specifying only the maximum number of total copies observed

  clusterdef.ncopies(n,
    R.mean = c(`0` = -3.527211, `1` = -0.664184, `2` = 0, `3` = 0.395621, `4` = 0.678345),
    R.sd = c(`0` = 1.329152, `1` = 0.284338, `2` = 0.159645, `3` = 0.209089, `4` = 0.191579),
    eps = 0.01)

`n`	maximum number of copies
`R.mean`	default values of LRR means for 0..4 copies
`R.sd`	default values of LRR sds for 0..4 copies
`eps`	distance from 0 or 1 to assign theta values with theoretical values of 0 or 1

Default values for LRR means and sd are taken from ???. The LRR_SD is quite dependent on data quality and normalisation but the LRR-Mean should be fairly good.

LRR_mean: Copy 0 1 2 3 4+ -3.527211 -0.664184 0.000000 0.395621 0.678345 LRR_sd: Copy 0 1 2 3 4+ 1.329152 0.284338 0.159645 0.209089 0.191579

a clusterdef object

Chris Wallace

chr1swallace/caller documentation built on May 13, 2019, 6:18 p.m.