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EstMix (version 1.0.1)

Tumor Clones Percentage Estimations

Description

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, for more details.

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Version

Install

install.packages('EstMix')

Monthly Downloads

80

Version

1.0.1

License

GPL (>= 2)

Maintainer

Xuan You

Last Published

September 13th, 2018

Functions in EstMix (1.0.1)

calculate likelihood for 1 normal + 2 tumors case

It is a function that takes the LRR obtained from SNP array data and returns the estimated tumor and normal proportions. Currently, the function can performs the proportion estimations by assuming the number of tumor clones to be 1 or 2 or 3. The normalization step is not required and the normalization constant will be returned by this function. The function will output two sets of solutions corresponding to the top 2 optimal solutions based on the posterior distribution. You can choose according to your expertise the one that is more reasonable.

est_mixture_wgs

It is a function that takes the count data obtained from whole genome sequencing (WGS) data and returns the estimated tumor and normal proportions. Currently, the function can performs the proportion estimations by assuming the number of tumor clones to be 1 or 2. The normalization step is not required and the normalization constant will be returned by this function. The function will output two sets of solutions corresponding to the top 2 optimal solutions based on the posterior distribution. You can choose according to your expertise the one that is more reasonable.

Return mixture estimation of a normal and a tumor Takes BAF, LRR, chr, x, gt, seg_raw

select scale for 1 normal + 1 tumor case

calculate baf_1d for 1 normal + 1 tumor case

get_segmentation

calculate segmentation

Return mixture estimation for percentage of normal cells and tumor (1 normal + 1 tumor) with wgs data Takes baf, lrr, n_baf and nrc

Return mixture estimation of a normal and 2 tumors Takes BAF, LRR, chr, x, gt, seg_raw

get_var_tcn_baf

get_var_tcn_baf

Return mixture estimation of a normal and 3 tumors Takes BAF, LRR, chr, x, gt, seg_raw

Return mixture estimation for percentage of normal cells and tumor (1 normal + 2 tumors) with wgs data Takes baf, lrr, n_baf and nrc

trancate data and take mean

Preprocessing data

calculate baf for 1 normal + 2 tumors case

calculate likelihood for 1 normal + 3 tumors case

combine_close_seg

combine close segmentation

sel_scale_1d_wgs

select scale for 1 normal + 1 tumor case for wgs data

sel_scale_2d_wgs

select scale for 1 normal + 2 tumors case for wgs data

select scale for 1 normal + 2 tumors case

calculate likelihood for 1 normal + 1 tumor case