Description Usage Arguments Value
Classify the binned read counts into several states which represent copy-number-variation. The function uses the e.divisive
function to segment the genome.
1 2 | edivisive.findCNVs(binned.data, ID = NULL, CNgrid.start = 1.5,
strand = "*", R = 10, sig.lvl = 0.1)
|
binned.data |
A GRanges-class object with binned read counts. |
ID |
An identifier that will be used to identify this sample in various downstream functions. Could be the file name of the |
CNgrid.start |
Start parameter for the CNgrid variable. Very empiric. Set to 1.5 for normal data and 0.5 for Strand-seq data. |
strand |
Find copy-numbers only for the specified strand. One of |
R |
method-edivisive: The maximum number of random permutations to use in each iteration of the permutation test (see |
sig.lvl |
method-edivisive: The level at which to sequentially test if a proposed change point is statistically significant (see |
An aneuHMM
object.
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