View source: R/Get_and_Filter_Regions.R
filterRegions | R Documentation |
filterRegions()
filters a region set using specified covMin
and
methSD
thresholds and then saves it as a tab-delimited text file.
filterRegions(
regions,
covMin = 10,
methSD = 0.05,
save = TRUE,
file = "Filtered_Regions.txt",
verbose = TRUE
)
regions |
A |
covMin |
A |
methSD |
A |
save |
A |
file |
A |
verbose |
A |
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.
A filtered version of the regions
data.frame
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.
## 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)
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