merge_scMethrix: Merges two 'scMethrix' objects by 'row' or 'col'

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

Description

Merges two scMethrix objects by row or col

Usage

merge_scMethrix(
  scm1 = NULL,
  scm2 = NULL,
  by = c("row", "column"),
  verbose = TRUE
)

Arguments

scm1	scMethrix; A single cell methylation experiment
scm2	scMethrix; A single cell methylation experiment
by	string; Merge by 'columns' or 'rows'
verbose	boolean; Flag for outputting function status messages. Default = TRUE

Details

Merges the assay data from two scMethrix objects. Assays not shared between assays will be dropped, as well as all reduced dimensionality data.

Requirements for merging

• If merging by rows, all CpG sites must be unique and samples must be identical

• If merging by columns, all samples must be unique and CpG sites must be identical

Metadata will be retained in certain situations: For row merges: - Ranges metadata (mcols()) will be merged, with missing columns in either assay filled with NAs - Sample metadata (colData()) will attempt to be merged. Overlapping, non-identical columns will be appended with .1 and .2.

For row merges: - Ranges metadata (mcols()) will attempt to be merged. Overlapping, non-identical columns will be appended with .1 and .2. - Sample metadata (colData()) will be merged, with missing columns in either assay filled with NAs

For both merges: - Experiment metadata (metadata()) will attempt to be merged. Overlapping, non-identical elements will be appended with .1 and .2.

Custom experiment metadata can manually be added via metadata() <-, or to rowRanges via mcols() <-.

Value

A merged scMethrix object

Examples

data('scMethrix_data')
merge_scMethrix(scMethrix_data[1:5],scMethrix_data[6:10],by="row")
merge_scMethrix(scMethrix_data[,1:2],scMethrix_data[,3:4],by="col")

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