Description Usage Value Author(s) Examples
This function sets the default values of parameters required to run sAGP estimation.
1 |
The default parameters obtained from this function is essential to run getsAGP()
. These parameters include:
inputdata |
full path to input data file generated by |
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 |
BAFfilter |
DNA segments with BAF markers below this value are removed to reduce noise. Default 10 |
thr.kmeans |
convergence threshold for |
thr.originsize |
minimum number of markers included in the origin cluster, used by |
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 |
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
1 2 3 4 5 6 7 8 9 10 | 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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