create_pairwise_master: Create pairwise comparisons

In hui-tony-zk/pairwiseMethyl: Pairwise Comparisons For Single-cell DNA Methylation Data

Description

Create pairwise comparisons between single-cells

Usage

create_pairwise_master(cpg, digital = TRUE, cores_to_use = 2,
  calcdiff = TRUE)

Arguments

cpg	A list of named data frames containing CpG calls. See details for required format of dataframes. Required.
digital	Whether or not to discard non-binary CpG calls. Useful in single-cells as it's very unlikely that a single-cell contains a heterozygous methylation call. Defaults to TRUE.
calcdiff	Whether or not to directly calculate the average difference (if TRUE), or to return a list of dataframes containing pairwise common CpGs (if FALSE). Defaults to TRUE. Usually you don't want false unless you wish to do something else with all the pairwise data
ncores	Number of cores to parallelize over. Defaults to 1

Details

Each dataframe containing CpG calls must have the following four columns: 1. Chromsome column, named "chr" 2. Start/Position column, named "start" 3. Percentage or fractional methylation column, named "meth" (between 0-100 or 0-1)

Value

A list of dataframes if calcdiff is FALSE. Otherwise, a dataframe containing the pairwise dissimiarlties if calcdiff is TRUE.

hui-tony-zk/pairwiseMethyl documentation built on May 3, 2019, 5:18 p.m.