filterRegions: Filter Regions

In cemordaunt/comethyl: An R Package for Weighted Region Comethylation Network Analysis

Filter Regions

Description

filterRegions() filters a region set using specified covMin and methSD thresholds and then saves it as a tab-delimited text file.

Usage

filterRegions(
  regions,
  covMin = 10,
  methSD = 0.05,
  save = TRUE,
  file = "Filtered_Regions.txt",
  verbose = TRUE
)

Arguments

regions	A data.frame output from getRegions() giving the set of regions and statistics for each region.
covMin	A numeric(1) specifying the minimum number of reads at CpGs in a region in any sample
methSD	A numeric(1) specifying the minimum methylation standard deviation in a region
save	A logical(1) indicating whether to save the data.frame
file	A character(1) giving the file name (.txt) for the saved data.frame
verbose	A logical(1) indicating whether messages should be printed.

Details

The purpose of this function is to use cutoffs for minimum coverage and methylation standard deviation guided by other functions and obtain a robust set of variably methylated regions. Computational resources are also a consideration for network construction, with region sets of 250K or less generally performing well.

Value

A filtered version of the regions data.frame

See Also

• getRegions() to generate the set of regions.

• plotRegionStats(), plotSDstats(), getRegionTotals(), and plotRegionTotals() for help visualizing region characteristics and setting cutoffs for filtering.

• getRegionMeth() to get methylation values for these regions in all samples.

Examples

## Not run: 

# Call Regions
regions <- getRegions(bs, file = "Unfiltered_Regions.txt")
plotRegionStats(regions, maxQuantile = 0.99,
                file = "Unfiltered_Region_Plots.pdf")
plotSDstats(regions, maxQuantile = 0.99,
            file = "Unfiltered_SD_Plots.pdf")

# Examine Region Totals at Different Cutoffs
regionTotals <- getRegionTotals(regions, file = "Region_Totals.txt")
plotRegionTotals(regionTotals, file = "Region_Totals.pdf")

# Filter Regions
regions <- filterRegions(regions, covMin = 10, methSD = 0.05,
                         file = "Filtered_Regions.txt")
plotRegionStats(regions, maxQuantile = 0.99,
                file = "Filtered_Region_Plots.pdf")
plotSDstats(regions, maxQuantile = 0.99,
            file = "Filtered_SD_Plots.pdf")

## End(Not run)

cemordaunt/comethyl documentation built on Oct. 20, 2023, 5:47 p.m.