metevalue.biseq {metevalue}

Calculate E-value of the BiSeq data format

Description

Please check vignette "metevalue" for details.

Usage

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

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

BiSeq.output

is the output file of BiSeq. The columns are (in order):

- seqnames: Chromosome

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

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

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

- strand: Strand

- median.p: The median p-value among CpG sites within the corresponding region

- median.meth.group1: The median methylation rate in the first group among CpG sites within the corresponding region

- median.meth.group2: The median methylation rate in the second group among CpG sites within the corresponding region

- median.meth.diff: The median methylation difference between groups among CpG sites within the corresponding region

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 BiSeq.output 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

#\donttest{
#data("demo_biseq_methyrate")
#data("demo_biseq_DMR")
#example_tempfiles = tempfile(c("demo_biseq_methyrate", "demo_biseq_DMR"))
#tempdir()
#### write to temp file ####
#write.table(demo_biseq_methyrate, file=example_tempfiles[1],row.names=FALSE,
#            col.names=TRUE, quote=FALSE, sep='\t')
#write.table(demo_biseq_DMR, file=example_tempfiles[2],
#             sep ="\t", row.names =FALSE, col.names =TRUE, quote =FALSE)
#### compute e-value and its adjustment ####
#result = metevalue.biseq(example_tempfiles[1],
#                         example_tempfiles[2], bheader = TRUE)
#}