classifyBAF: Cluster BAF values using given cluster centers, a helper...
In aksenia/SeeCiTe: Assess the quality of and visualize array CNV callset for trios
Description
Usage
Arguments
Value
Description
Cluster BAF values using given cluster centers, a helper function
Usage
1
classifyBAF(mybaf, margin.dup = 0.05, margin.het = 0.1, margin.nh = 0.17)
Arguments
mybaf
The input data table collated with readSiftInput for individual CNV and sample in "data"
margin.dup
A margin value around dup clusters AAB or ABB (0.33 and 0.66). Default is 0.05.
margin.het
A margin value around heterozygous AB cluster (0.5). Default is 0.1.
margin.nh
A margin value around homozygous AA or BB clusters (0 and 1). Default is 0.17
Value
A data table with counts and fractions of probes in each cluster defined by the arguments and copynumber status derived based on those, one of "BAFagreeNormal", "possiblyLOH" or "BAFsuggDup".
aksenia/SeeCiTe documentation built on Jan. 19, 2021, 12:35 a.m.
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Description Usage Arguments Value
Description
Cluster BAF values using given cluster centers, a helper function
Usage
1 | classifyBAF(mybaf, margin.dup = 0.05, margin.het = 0.1, margin.nh = 0.17)
|
Arguments
mybaf |
The input data table collated with readSiftInput for individual CNV and sample in "data" |
margin.dup |
A margin value around dup clusters AAB or ABB (0.33 and 0.66). Default is 0.05. |
margin.het |
A margin value around heterozygous AB cluster (0.5). Default is 0.1. |
margin.nh |
A margin value around homozygous AA or BB clusters (0 and 1). Default is 0.17 |
Value
A data table with counts and fractions of probes in each cluster defined by the arguments and copynumber status derived based on those, one of "BAFagreeNormal", "possiblyLOH" or "BAFsuggDup".
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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