filterGRange: Filter methylation counts by coverage in a GRanges object

In genomaths/MethylIT: Methylation Analysis Based on Signal Detection

Filter methylation counts by coverage in a GRanges object

Description

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'.

Usage

filterGRange(
  x,
  min.coverage = 4,
  max.coverage = Inf,
  percentile = 0.999,
  col.names = c(coverage = NULL, mC = NULL, uC = NULL),
  sample.name = "",
  verbose = TRUE
)

Arguments

x	GRanges object
min.coverage	Cytosine sites with coverage less than min.coverage are discarded. Default: 0
max.coverage	Cytosine sites with coverage greater than max.coverage are discarded. Default: Inf
percentile	Threshold to remove the outliers from each file and all files stacked. If percentile is 1, all the outliers stay
col.names	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.
sample.name	Name of the sample
verbose	If TRUE, prints the function log to stdout

Details

The input must be a GRanges object with a coverage column in the metacolumn table or the columns with methylated (mC) and unmethylated counts (uC).

Value

The input GRanges object or list of GRanges objects after filtering it.

Examples

    gr1 <- makeGRangesFromDataFrame(
        data.frame(chr = 'chr1', start = 11:15, end = 11:15,
                strand = c('+','-','+','*','.'), mC = 1, uC = 1:5),
        keep.extra.columns = TRUE)
    filterGRange(gr1, min.coverage = 1, max.coverage = 4,
                col.names = c(mC = 1, uC = 2), verbose = FALSE)

genomaths/MethylIT documentation built on Feb. 3, 2024, 1:24 a.m.