Tumor Clones Percentage Estimations
Return mixture estimation of a normal and a tumor Takes BAF, LRR, chr,...
Return mixture estimation for percentage of normal cells and tumor (1 ...
Return mixture estimation of a normal and 2 tumors Takes BAF, LRR, chr...
Return mixture estimation for percentage of normal cells and tumor (1 ...
Return mixture estimation of a normal and 3 tumors Takes BAF, LRR, chr...
return sqrt(n)
calculate baf_1d for 1 normal + 1 tumor case
calculate baf for 1 normal + 2 tumors case
calculate likelihood for 1 normal + 2 tumors case
calculate likelihood for 1 normal + 1 tumor case
calculate likelihood for 1 normal + 3 tumors case
combine close segmentation
It is a function that takes the LRR obtained from SNP array data and r...
It is a function that takes the count data obtained from whole genome ...
f_baf
calculate segmentation
get_var_tcn_baf
trancate data and take mean
Preprocessing data
select scale for 1 normal + 1 tumor case
select scale for 1 normal + 1 tumor case for wgs data
select scale for 1 normal + 2 tumors case
select scale for 1 normal + 2 tumors case for wgs data
Includes R functions for the estimation of tumor clones percentages for both snp data and (whole) genome sequencing data. See Cheng, Y., Dai, J. Y., Paulson, T. G., Wang, X., Li, X., Reid, B. J., & Kooperberg, C. (2017). Quantification of multiple tumor clones using gene array and sequencing data. The Annals of Applied Statistics, 11(2), 967-991, <doi:10.1214/17-AOAS1026> for more details.