metevalue.DMRfinder.chk {metevalue}

Check the DMRfinder data format

Description

Check the DMRfinder data format

Usage

metevalue.DMRfinder.chk(
  input_filename_a,
  input_filename_b,
  sep = "\t",
  bheader = FALSE
)

Arguments

input_filename_a

the combined data of methylation rate file. This file is a sep (e.g. TAB) separated file with two key columns and several value columns. For exampe:

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

The columns are (in order):

- chr and pos are keys;

- g1~g2: methylation rate data in groups.

input_filename_b

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

- chr: Chromosome

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

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

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

- 'Control:mu': The absolute mean methylation level for the corresponding segment of the control group

- 'Exptl:mu': The absolute mean methylation level for the corresponding segment of the experimental group

- 'Control->Exptl:diff': The difference between the group means of methylation level

- p: p-value

sep

separator, 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

list(file_a, file_b, file_a_b) returns a list with three pr-handled data.frames corresponding to the input_filename_a, input_filename_b file and a A JOIN B file.

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.chk(example_tempfiles[1], example_tempfiles[2],
#      bheader = TRUE)