calc_1d_wgs

a numeric vector. Each element is the mean adjusted B allele frequency for that segment, calculated as the mean of baf_tumor/baf_normal/2 for that segment

a numeric vector. Each element is the log ratio of the tumor read count and the normal read count for a segment, defined as log(tumorCount/normalCount)

n_baf

a numeric vector. Each element is the normal read count of the segment divided by two

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

internal

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.

Xuan You

EstMix

Tumor Clones Percentage Estimations

calc_1d_wgs function

Return mixture estimation for percentage of normal cells and tumor (1 normal + 1 tumor) with wgs data
Takes <code>baf</code>, <code>lrr</code>, <code>n_baf</code> and <code>nrc</code> — calc_1d_wgs

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

calc_1d_wgs: Return mixture estimation for percentage of normal cells and tumor (1 normal + 1 tumor) with wgs data Takes `baf`, `lrr`, `n_baf` and `nrc`

Description

Usage

Arguments

Value