Initialize parameters for sAGP estimation.

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Description

This function sets the default values of parameters required to run sAGP estimation.

Usage

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Value

The default parameters obtained from this function is essential to run getsAGP(). These parameters include:

inputdata

full path to input data file generated by getSeg() or in the same format

savedata

name of the output plain text file to be saved

pngdir

directory to save BAF-LRR plots, ignored if is.png is FALSE

purityfile

AGP estimation file returned by getAGP()

BAFfilter

DNA segments with BAF markers below this value are removed to reduce noise. Default 10

thr.kmeans

convergence threshold for getKmeans(). Default 0.1

thr.originsize

minimum number of markers included in the origin cluster, used by getOrigin(). Default 500

thr.penalty

penalty (in units of number of markers) to increase ploidy. Default 500

std.BAF

standard deviation of BAF markers. Default 0.025

std.LRR

standard deviation of LRR markers. Default 0.1

is.normalize

if data needs to be normalized first. Default TRUE

LRR_correction_del

factor to correct negative LRR values. Default 0.572

LRR_correction_amp

factor to correct positive LRR values. Default 0.553

K

constant parameter for objective function F (see details in getSegPurity()). Default 12

is.plot

if TRUE, the process of estimating sAGP value for each data point will be shown on a prompted BAF-LRR plot. Default FALSE

max.cn

maximum copy number examined. Default ploidy+4

strictness

maximum sAGP value considered during optimization. By allowing it to be larger than 1, small noise around 1 could be tolerated. Default 1.1

is.multicore

if to use multiple thread to increase computational speed. Default FALSE.

Author(s)

Bo Li

Examples

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para.s=getPara.sAGP()
## Increase strictness
para.s$strictness=1
## Not run: 
## Use multi-thread computing
install.packages('multicore')
library(multicore)
para.s$is.multicore=TRUE

## End(Not run)

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