varevalue.single_general {metevalue}

A general method to calculate the e-value for other DNA methylation tools not described above. The input data is the DNA methylation rates using the similar format with Metilene.

Description

The input data file is just the DNA methylation rates using the similar format above, with no need for another data file output by different tools. The Chromosome name, start and end sites shoule be specified in the function.

Usage

varevalue.single_general(
  methyrate,
  group1_name = "g1",
  group2_name = "g2",
  chr,
  start,
  end
)

Arguments

methyrate

data.frame: A data.frame object of methylation rates, the columns should be (name of groups can be self-defined)

chr	pos	g1	...	g1	g2	...	g2
chr1	1	0.1	...	0.1	0.2	...	0.2

group1_name

charactor: The name (pattern) of the first group. For example, "g1" in the above example. For example 'g1_abc' and 'g1' will be considered as the same group if 'group1_name = "g1"'. Use this with care in practice.

group2_name

charactor: The name (pattern) of the second group. For example, "g2" in the above example. For example 'g2_abc' and 'g2' will be considered as the same group if 'group2_name = "g2"'. Use this with care in practice.

chr

charactor: The Chromosome name. Typically, it is a string like "chr21" and so on.

start

integer: The position of the start site of the corresponding region

end

integer: The position of the end site of the corresponding region

Value

evalue

Examples

#data("demo_metilene_input")
#varevalue.single_general(demo_metilene_input, chr = "chr21", start = 9437432, end = 9437540)
# [1] 2.626126e+43

#### Compare to `metevalue.metilene`  ####
data(demo_metilene_out)
#example_tempfiles = tempfile(c("metilene_input", "metilene_out"))
#tempdir()
#write.table(demo_metilene_input, file=example_tempfiles[1],
#      row.names=FALSE, col.names=TRUE, quote=FALSE, sep='\t')
#write.table (demo_metilene_out, file=example_tempfiles[2],
#      sep ="\t", row.names =FALSE, col.names =TRUE, quote =FALSE)
#result = metevalue.metilene(example_tempfiles[1], example_tempfiles[2],
#      bheader = TRUE)
# result[with(result, chr == 'chr21' & start == '9437432' & end == '9437540'), ncol(result)]
# [1] 2.626126e+43