runMiMMAl: The main MiMMAl function.

Description Usage Arguments Examples

View source: R/MiMMAl-function.R

Description

This function takes segmented BAF data as input and models the major and minor allele distributions.

Usage

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runMiMMAl(samplename, inputfile, min.snps = 10, sd.width = 1/3,
  preset.sd = NULL, seed = 1, baf.res = 2, use.ks.gate = TRUE,
  plot.sd.den = TRUE, plot.lit.plot = TRUE, plot.star.plot = TRUE,
  plot.transformed = TRUE)

Arguments

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.

Examples

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georgecresswell/MiMMAl documentation built on Oct. 25, 2020, 2:40 p.m.