metevalue.methylKit {metevalue}

Calculate E-value of the methylKit data format

Description

Calculate E-value of the methylKit data format

Usage

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

Arguments

methyrate

is the data of methylation rates of each sites and group. 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

methylKit.output

is the output data with e-value of each region

- chr: Chromosome

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

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

- strand: Strand

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

- qvalue: cutoff for qvalue of differential methylation statistic

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

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 input_filename_b file contains the names of the variables as its first line. By default, 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

Examples

data(demo_methylkit_methyrate)
data(demo_methylkit_met_all)
## example_tempfiles = tempfile(c("rate_combine", "methylKit_DMR_raw"))
## tempdir()
## write.table(demo_methylkit_methyrate, file=example_tempfiles[1],
##       row.names=FALSE, col.names=TRUE, quote=FALSE, sep='\t')
## write.table(demo_methylkit_met_all, file=example_tempfiles[2],
##       sep ="\t", row.names =FALSE, col.names =TRUE, quote =FALSE)
## result = metevalue.methylKit(example_tempfiles[1], example_tempfiles[2],
##       bheader = TRUE)
## str(result)