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)
Value
Either a data.table of filtered data with additional columns for Coverage and Variance or a list of matrices of filtered data
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)
Examples
if (FALSE) { # \dontrun{
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
} # }