create_melissa_data_obj: Create methylation regions for all cells

In andreaskapou/Melissa: Bayesian clustering and imputationa of single cell methylomes

Description

Wrapper function for creating methylation regions for all cells, which is the input object for Melissa prior to filtering.

Usage

create_melissa_data_obj(
  met_dir,
  anno_file,
  chrom_size_file = NULL,
  chr_discarded = NULL,
  is_centre = FALSE,
  is_window = TRUE,
  upstream = -5000,
  downstream = 5000,
  cov = 5,
  sd_thresh = -1,
  no_cores = NULL
)

Arguments

met_dir	Directory of (binarised) methylation files, each file corresponds to a single cell.
anno_file	The annotation file with 'tab' delimited format: "chromosome", "start", "end", "strand", "id", "name" (optional). Read the 'BPRMeth' documentation for more details.
chrom_size_file	Optional file name to read genome chromosome sizes.
chr_discarded	Optional vector with chromosomes to be discarded.
is_centre	Logical, whether 'start' and 'end' locations are pre-centred. If TRUE, the mean of the locations will be chosen as centre. If FALSE, the 'start' will be chosen as the center; e.g. for genes the 'start' denotes the TSS and we use this as centre to obtain K-bp upstream and downstream of TSS.
is_window	Whether to consider a predefined window region around centre. If TRUE, then 'upstream' and 'downstream' parameters are used, otherwise we consider the whole region from start to end location.
upstream	Integer defining the length of bp upstream of 'centre' for creating the genomic region. If is_window = FALSE, this parameter is ignored.
downstream	Integer defining the length of bp downstream of 'centre' for creating the genomic region. If is_window = FALSE, this parameter is ignored.
cov	Integer defining the minimum coverage of CpGs that each region must contain.
sd_thresh	Optional numeric defining the minimum standard deviation of the methylation change in a region. This is used to filter regions with no methylation variability.
no_cores	Number of cores to be used for parallel processing of data.

Value

A melissa_data_obj object, with the following elements:

• met: A list of elements of length N, where N are the total number of cells. Each element in the list contains another list of length M, where M is the total number of genomic regions, e.g. promoters. Each element in the inner list is an I X 2 matrix, where I are the total number of observations. The first column contains the input observations x (i.e. CpG locations) and the 2nd column contains the corresponding methylation level.

• anno_region: The annotation object.

• opts: A list with the parameters that were used for creating the object.

Author(s)

C.A.Kapourani [e-mail]

See Also

binarise_files, melissa, filter_regions

Examples

## Not run: 
# Met directory
met_dir <- "name_of_met_dir"
# Annotation file name
anno_file <- "name_of_anno_file"

obj <- create_melissa_data_obj(met_dir, anno_file)

# Extract annotation regions
met <- obj$met

# Extract annotation regions
anno <- obj$anno_region

## End(Not run)

andreaskapou/Melissa documentation built on June 12, 2020, 5:54 p.m.