Description Usage Value Author(s) Examples
This function sets default values to parameters required to run AGP estimation.
1 | getPara()
|
The default parameters obtained from this function is essential to run getAGP()
. These parameters include:
datafile |
full path to input data file generated by |
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 |
thr.originsize |
minimum number of markers included in the origin cluster, used by |
thr.CL |
threshold distance to call a data point to be close to a canonical line, used by |
thr.CP |
threshold distance to call a data point to be close to a canonical point, used by |
thr.penalty |
penalty (in units of number of markers) to increase ploidy. Default 500 |
std.BAF |
standard deviation of BAF markers. Default 0.02 |
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 |
Bo Li
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