The function is used to discard the cytosine positions with coverage values less than 'min.coverage' read counts or values greater than the specified 'percentile'.
filterByCoverage(
x,
min.coverage = 4,
max.coverage = Inf,
percentile = 0.999,
col.names = c(coverage = NULL, mC = NULL, uC = NULL),
verbose = TRUE
)GRanges object or list of GRanges
Cytosine sites with coverage less than min.coverage are discarded. Default: 0
Cytosine sites with coverage greater than max.coverage are discarded. Default: Inf
Threshold to remove the outliers from each file and all files stacked. If percentile is 1, all the outliers stay
The number of the 'coverage' column. Since no specific table format for the count data is specified, at least the number of the 'coverage' column must be given, or the number of the columns with methylated (mC) and unmethylated counts (uC). Then coverage = mC + uC.
If TRUE, prints the function log to stdout
The input GRanges object or list of GRanges objects after filtering them.
The input must be a GRanges object or list of GRanges objects with a coverage column in the meta-column table or the columns with methylated (mC) and unmethylated counts (uC).
gr1 <- makeGRangesFromDataFrame(data.frame(chr = 'chr1', start = 11:15,
end = 11:15, strand = c('+','-','+','*','.'), mC = 1, uC = 1:5),
keep.extra.columns = TRUE)
filterByCoverage(gr1, min.coverage = 1, max.coverage = 4,
col.names = c(mC = 1, uC = 2), verbose = FALSE)
#> GRanges object with 2 ranges and 2 metadata columns:
#> seqnames ranges strand | mC uC
#> <Rle> <IRanges> <Rle> | <numeric> <integer>
#> [1] chr1 11 + | 1 1
#> [2] chr1 12 - | 1 2
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths