getPara.sAGP: Initialize parameters for sAGP estimation.
In Shicheng-Guo/CHAT: Clonal Heterogeneity Analysis Tool

Description Usage Value Author(s) Examples

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

1	getPara.sAGP()

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.

Bo Li

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)