getPara: Initialize parameters for AGP estimation

In CHAT: Clonal Heterogeneity Analysis Tool

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

Author(s)

Bo Li

Examples

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

CHAT documentation built on May 29, 2017, 10:32 p.m.