Get Total CpGs at Different Coverage Cutoffs

getCpGtotals() calculates the total number and percent of CpGs remaining in a BSseq object after filtering at different cov and perSample cutoffs and then saves it as a tab-delimited text file.

Usage

getCpGtotals(
  bs,
  cov = seq(0, 10, 1),
  perSample = seq(0.5, 1, 0.05),
  save = TRUE,
  file = "CpG_Totals.txt",
  verbose = TRUE
)

Arguments

bs: A BSseq object.
cov: A numeric specifying the minimum number of reads overlapping a CpG for it to be included in the total.
perSample: A numeric specifying the minimum percent of samples with cov reads at a CpG for it to be included in the total.
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.

Value

A data.frame giving the number of CpGs (in millions) and the percent of total CpGs at all combinations of cov and perSample. The number of samples corresponding to perSample is also given.

Details

The purpose of this function is to help determine cutoffs to maximize the number of CpGs with sufficient data after filtering. It's recommended to input multiple cov and perSample cutoffs for comparison. Typically, the number of CpGs covered in 100% of samples decreases as the sample size increases, especially with low-coverage datasets.

Examples

if (FALSE) {

# Read Bismark CpG Reports
colData <- read.xlsx("sample_info.xlsx", rowNames = TRUE)
bs <- getCpGs(colData, file = "Unfiltered_BSseq.rds")

# Examine CpG Totals at Different Cutoffs
CpGtotals <- getCpGtotals(bs, file = "CpG_Totals.txt")
plotCpGtotals(CpGtotals, file = "CpG_Totals.pdf")

# Filter BSseq Object
bs <- filterCpGs(bs, cov = 2, perSample = 0.75, file = "Filtered_BSseq.rds")
}