metevalue (version 0.2.4)

metevalue.DMRfinder: Calculate E-value of the DMRfinder data format

Description

Calculate E-value of the DMRfinder data format

Usage

metevalue.DMRfinder(
  methyrate,
  DMRfinder.output,
  adjust.methods = "BH",
  sep = "\t",
  bheader = FALSE
)

Value

a dataframe, the columns are (in order):

- chr: Chromosome

- start: The positions of the start sites of the corresponding region

- end: The positions of the end sites of the corresponding region

- q-value: The adjusted p-value based on BH method in MWU-test

- methyl.diff: The difference between the group means of methylation level

- CpGs: The number of CpG sites within the corresponding region

- p : p-value based on MWU-test

- p2: p-value based on 2D KS-test

- m1: The absolute mean methylation level for the corresponding segment of group 1

- m2: The absolute mean methylation level for the corresponding segment of group 2

- e_value: The e-value of the corresponding region

Arguments

methyrate

is the methyrate file. For example:

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

The columns are (in order):

- chr: Chromosome

- pos: int Position

- g1~g2: methylation rate data in groups

DMRfinder.output

is the output file of DMRfinder.

- chr: Chromosome

- start: The positions of the start sites of the corresponding region

- end: The positions of the end sites of the corresponding region

- CpG: The number of CpG sites within the corresponding region

- Control.mu: The average methylation rate in control group

- Expt1.mu: The average methylation rate in experiment group

- Control.Expt1.diff: The methylation difference between control and experiment groups

- Control.Expt1.pval: P-value based on Wald-test.

adjust.methods

is the adjust methods of e-value. It can be 'bonferroni', 'hochberg', 'holm', 'hommel', 'BH', 'BY'

sep

seperator, default is the TAB key.

bheader

a logical value indicating whether the DMRfinder.output file contains the names of the variables as its first line. By default, bheader = FALSE.

Examples

data(demo_DMRfinder_rate_combine)
data(demo_DMRfinder_DMRs)
#example_tempfiles = tempfile(c("rate_combine", "DMRfinder_out"))
#tempdir()
#write.table(demo_DMRfinder_rate_combine, file=example_tempfiles[1],
#      row.names=FALSE, col.names=TRUE, quote=FALSE, sep='\t')
#write.table(demo_DMRfinder_DMRs, file=example_tempfiles[2],
#      sep ="\t", row.names =FALSE, col.names =TRUE, quote =FALSE)
#result = metevalue._DMRfinder(example_tempfiles[1], example_tempfiles[2],
#      bheader = TRUE)
#head(result)