varevalue.single_general: A general method to calculate the e-value for other DNA...

In metevalue: E-Value in the Omics Data Association Studies

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

metevalue documentation built on May 31, 2023, 8:19 p.m.