loadAllData

A character vector with the paths to all bam files

files

Either a GRanges or data.frame with the coordinates of interest

regions

Number of cores used for loading, default = 1

mc.cores


This function uses the parallel package and the bam2R interface to load all nucleotide counts from a list of bam files and a set of regions into a large array.


This package provides provides quantitative variant callers for
detecting subclonal mutations in ultra-deep (>=100x coverage) sequencing
experiments. The deepSNV algorithm is used for a comparative setup with a
control experiment of the same loci and uses a beta-binomial model and a
likelihood ratio test to discriminate sequencing errors and subclonal SNVs.
The shearwater algorithm computes a Bayes classifier based on a
beta-binomial model for variant calling with multiple samples for
precisely estimating model parameters such as local error rates and
dispersion and prior knowledge, e.g. from variation data bases such as
COSMIC.

Moritz Gerstung

deepSNV

Detection of subclonal SNVs in deep sequencing data.

loadAllData function

This function uses the parallel package and the bam2R interface to load all nucleotide counts from a list of bam files and a set of regions into a large array.

loadAllData: Function to load all data from a list of bam files

Description

Usage

Arguments

Value