Description Usage Arguments Value
View source: R/paper_functions.R
Calculate the amount of overlap between the CN and BAF inferred drift GRanges objects
1 2 3 4 5 6 7 8 9 | driftOverlapMetric(
gr.baf,
gr.cn,
cell.ids,
ov.frac = seq(0, 1, by = 0.01),
baf.z = 4,
cn.z = 2,
cn.gtruth = FALSE
)
|
gr.baf |
GRangesList of cell lines an their BAF-drifted regions |
gr.cn |
GRangesList of cell lines an their CN-drifted regions |
cell.ids |
Vector of cell line names to check drift of |
ov.frac |
overlap fraction cutoff: (Default: seq(0, 1, by=0.01)) |
baf.z |
z threshold for BAF difference |
cn.z |
z threshold for L2R difference |
cn.gtruth |
if TRUE, isolates BAF for only CN drifted regions |
List containing the following elements: "model" = non-linear least-square model fitted to concordance and sensitvity "saturation"=Matrix of total saturation and concordance cutoff "sens"=Matrix of sensitivity value for each concordance cutoff "dat"=Matrix of concordance cutoff by cell lines
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