get_matrix: Extract assays from an 'scMethrix' object

In CompEpigen/scMethrix: Fast and efficient summarization of single cell whole genome bisulfate data

Description

Extract assays from an scMethrix object

Usage

get_matrix(
  scm = NULL,
  assay = "score",
  add_loci = FALSE,
  in_granges = FALSE,
  order_by_sd = FALSE,
  n_chunks = 1,
  by = c("row", "column")
)

Arguments

scm	scMethrix; the single cell methylation experiment
assay	string; name of an existing assay. Default = "score"
add_loci	Default FALSE. If TRUE adds CpG position info to the matrix and returns as a data.table
in_granges	Do you want the outcome in GRanges?
order_by_sd	Order output matrix by standard deviation
n_chunks	integer; Number of chunks to split the scMethrix object in case it is very large. Default = 1
by	string; split the matrix by "row" or "col" if n_chunks != 1

Details

Takes scMethrix object and returns the methylation matrix. This will return in the format used by the object (matrix or HDF5matrix).

Value

HDF5Matrix or matrix

Examples

data('scMethrix_data')

# Get methylation data
get_matrix(scMethrix_data)

# Get methylation data with loci
get_matrix(scMethrix_data, add_loci=TRUE)

# Get methylation data with loci inside a Granges object 
get_matrix(scMethrix_data, add_loci=TRUE, in_granges=TRUE)

# Get methylation data sorted by SD
get_matrix(scMethrix_data, order_by_sd = TRUE)

# Split the matrix into parts
get_matrix(scMethrix_data, n_chunks = 4, by="row")

CompEpigen/scMethrix documentation built on Nov. 6, 2021, 3:09 p.m.