mag.reduce.graph: MAG REDUCE STEP

In liliulab/magos: Model-based Adaptive Grouping of Subclones

MAG REDUCE STEP

Description

This function is used to create a pre clustering merging of the data. This function is used to merge data points that are close to each other using a graph approach.

Usage

mag.reduce.graph(prep.data, x.el = matrix(), n = -100, threshold = 0.03)

Arguments

prep.data	Preproccessed dataframe of the data.
x.el	A dataframe of samples that want to be forced together. Each row coresponds to a cluster and each column represents a data point (mutation). This is a 0-1 matrix. Sum of each column should be 1 and sum of each row should be number of mutations in that cluster. At step 0, where each mutation is a cluster, this dataframe is a m*m matrix with 1s on the diagonal. The default is an empty dataframe but the function populates this dataframe.
n	This variable is used internaly. Do not change it.
threshold	This parameter is used to merge mutations that their VAF difference is less than the threshold. Default is 0.03. Meaning in the reduce step, in order to speed up the process, the mutations that their max VAF distance is 0.03 are merged together.

Value

A list of files. x.el.red is the main output of the function. It is the update dataframe of clusters and mutations after performing the initial merging.

liliulab/magos documentation built on June 1, 2024, 3:31 a.m.