Description Usage Arguments Examples
View source: R/MiMMAl-function.R
This function takes segmented BAF data as input and models the major and minor allele distributions.
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samplename |
The output name for your sample. |
inputfile |
The file to be read in as containing the columns; chr, pos, BAF, BAFseg. |
min.snps |
Minimum number of SNPs to model. Default = 10. |
sd.width |
This value is multiplied by the chosen sd and the tested sd range is determined as the sdĀ±sd.width. Default = 1/3. |
preset.sd |
Add a float value for the standard deviation if it is to be preset, without this it 'learns' the sd. Default = NULL. |
seed |
Seed set for reproducibility. Default = 1. |
baf.res |
10^-baf.res is used as the size of the steps used in the grid search for testing BAF values. Default = 2. |
use.ks.gate |
Require the data to pass a normality test before modelling. Default = TRUE. |
plot.sd.den |
Plot the sd density plot? Default = TRUE. |
plot.lit.plot |
Plot the global grid search? Default = TRUE. |
plot.star.plot |
Plot the local grid search? Default = TRUE. |
plot.transformed |
Plot the transformed data? Default = TRUE. |
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