create_region_object: Create genomic region data

In geneprophet/BSDMR: a region-based method for quantitating the conservation and divergence of methylation patterns between species by high order features

Description

create_region_object creates genomic regions (e.g. forms methylation regions data) using as input methylation and annotation data with genomic regions of interest.

Usage

create_region_object(
  met_dt,
  anno_dt,
  cov = 5,
  ignore_strand = TRUE,
  is_parallel = TRUE,
  no_cores = NULL
)

Arguments

met_dt	A GRanges object with methylation data, whose format should be similar to read_methylation_report.
anno_dt	A GRanges object with annotation data, whose format should be similar to read_annotation.
cov	Integer defining the minimum coverage of CpGs that each region must contain.
ignore_strand	Logical, whether or not to ignore strand information.
is_parallel	Logical, indicating if code should be run in parallel.
no_cores	if you have specify the is_parallel is ture ,you can specify the number of parallel cores

Value

A list object containing the two elements:

• met: A list containing methylation region data, where each entry in the list is an L_{i} X D dimensional matrix, where L_{i} denotes the number of CpGs found in region i. The columns contain the following information:

  1. 1st column: Contains the locations of CpGs relative to centre. Note that the actual locations are scaled to the [-1,1] region.

  2. 2nd column: Contains the total number of reads at each CpG location.

  3. 3rd column: Contains the methylated reads at each CpG location.

  . Rownames of each matrix contain the actual CpG genomic coordinates as <chr>:<location>.

• anno: The annotation object.

Note: The lengths of met and anno should match.

Author(s)

Hongen Kang [e-mail]

See Also

read_methylation_report, read_annotation

Examples

## Not run: 
# Download the files and change the working directory to that location
human_met <- read_methylation_report("name_of_met_file")
human_anno <- read_annotation("name_of_anno_file")
human_obj <- create_region_object(human_met, human_anno)

## End(Not run)

geneprophet/BSDMR documentation built on March 3, 2021, 5:50 a.m.