make.ddclone.input: Generate a ddClone input object from bulk allele counts and...

In sohrabsa/ddclone: Joint statistical inference of clonal populations from single cell and bulk tumour sequencing data

Description

Generate a ddClone input object from bulk allele counts and single cell data and saves it in bulkDataPath.

Usage

make.ddclone.input(bulkData, genDat, outputPath, nameTag = "")

Arguments

bulkData	Path A dataframe that contains allele counts and copy number data. Expects colnames to be "mutation_id", "ref_counts", "var_counts", "normal_cn", "minor_cn", and "major_cn". "minor_cn" and "major_cn" should be integer values for the minimum and maxmum estimated copy number at that locus respectively.
outputPath	What directory should the output be saved into.
nameTag	An optional string to be appended to the name of the output object
genotypeMatrix	A binary matrix where rows correspond to genotypes and coloumns to mutation IDs respectively.

Value

A list with appropriate members that could be given as input for ddClone analysis, for instance ddclone::ddclone

sohrabsa/ddclone documentation built on May 30, 2019, 6:08 a.m.