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CHAT (version 1.1)

getPara.sAGP: Initialize parameters for sAGP estimation.

Description

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

Usage

getPara.sAGP()

Arguments

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.

Examples

Run this code
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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