CHAT (version 1.1)

getPara: Initialize parameters for AGP estimation

Description

This function sets default values to parameters required to run AGP estimation.

Usage

getPara()

Value

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

datafile

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

savefile

name of the output plain text file to be saved

pngdir

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

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.CL

threshold distance to call a data point to be close to a canonical line, used by getSumDist(). Default 0.05

thr.CP

threshold distance to call a data point to be close to a canonical point, used by getSumDist(). Default 0.05

thr.penalty

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

std.BAF

standard deviation of BAF markers. Default 0.02

std.LRR

standard deviation of LRR markers. Default 0.08

exclude.chr

chromosomes to be excluded from the analysis. Default NULL

res.r

resampling ratio for bootstrap. Default 0.8

num.tracks

number of canonical tracks to be considered in likelihood estimation. Default 4

is.normalize

if data needs to be normalized first. Default TRUE

is.perm

if bootstrap based null distribution of AGP is estimated, time consuming. Default FALSE

is.png

if BAF-LRR plots are saved. Default TRUE

is.plot

if BAF-LRR plots are shown during the process of AGP estimation. 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

Examples

para=getPara()
## Change threshold for ploidy increase
para$thr.penalty=200
## Skip png plotting
para$is.png=FALSE