read_bismark: Read in and Filter Bismark Coverage Files

In jcalendo/coriell: Convenience Functions for Bioinformatics

Read in and Filter Bismark Coverage Files

Description

This function will read in Bismark coverage files and optionally filter for coverage and feature-wise variance.

Usage

read_bismark(
  files,
  coverage = 1,
  prop_samples = 1,
  remove_zero_var = FALSE,
  return_mats = FALSE
)

Arguments

files	Named vector of file paths to the bismark coverage files
coverage	Minimum coverage for a CpG site. Default (1)
prop_samples	Proportion of samples that site must be covered to be retained. Default (1)
remove_zero_var	Should zero variance features be removed after filtering for coverage? Default (FALSE)
return_mats	if TRUE, return matrices of the filtered data in a list. Else, return the filtered data.table in bismark format. Default (FALSE)

Details

The function can optionally return a list of CpG x Sample matrices of the filtered data if return_mats = TRUE. The following matrices will be returned for each of the retained CpG sites: Coverage, Percent Methylation (Percent), count of methylated CpGs (Methylated) and count of unmethylated CpGs (Unmethylated)

Value

Either a data.table of filtered data with additional columns for Coverage and Variance or a list of matrices of filtered data

Examples

## Not run: 
files <- c("P6_1.bismark.cov.gz", "P6_4.bismark.cov.gz", "P7_2.bismark.cov.gz", "P7_5.bismark.cov.gz", "P8_3.bismark.cov.gz", "P8_6.bismark.cov.gz")
names(files) <- gsub("\\.bismark\\.cov\\.gz", "", files)

# Read in all files using default parameters -- returns a data.table
result <- read_bismark(files)

# Filter for coverage >= 20 in at least 50% of samples and remove any zero variance features
dt <- read_bismark(files, coverage = 20, prop_samples = 0.5, remove_zero_var = TRUE)

# Same filtering as above but return a list of CpG x Sample matrices
l <- read_bismark(files, coverage = 20, prop_samples = 0.5, remove_zero_var = TRUE, return_mats = TRUE)

# To view the CpG x Sample Coverages:
l$Coverage

# Percent methylation
l$Percent

## End(Not run)

jcalendo/coriell documentation built on March 5, 2025, 5:42 a.m.