Package: EstMix 1.0.1

Xuan You

EstMix: Tumor Clones Percentage Estimations

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.

Authors:Xuan You <[email protected]>, Yichen Cheng <[email protected]>

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EstMix/json (API)

# Install 'EstMix' in R:

install.packages('EstMix', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Uses libs:

c++– GNU Standard C++ Library v3

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

cpp

1.00 score 2 scripts 150 downloads 23 exports 16 dependencies

Last updated 6 years agofrom:1f28efc3a1. Checks:2 OK. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Feb 09 2025
R-4.5-linux-x86_64	OK	Feb 09 2025

Exports:calc_1d calc_1d_wgs calc_2d calc_2d_wgs calc_3d calc_n calcll_1d_baf calcll_baf calcll_cpp calcll_p1_cpp calcll_p3 combine_close_seg est_mixture est_mixture_wgs f_baf get_segmentation get_var_tcn_baf mean2 preprocessing sel_scale_1d sel_scale_1d_wgs sel_scale_2d sel_scale_2d_wgs

Dependencies:aroma.light codetools digest DNAcopy future globals listenv matrixStats parallelly PSCBS R.cache R.methodsS3 R.oo R.utils Rcpp RcppArmadillo

Help page	Topics
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
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.	est_mixture_wgs

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

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.

est_mixture_wgs

Package: EstMix 1.0.1

EstMix: Tumor Clones Percentage Estimations

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