metevalue.methylKit.chk {metevalue}

Check the methylKit data format

Description

Check the methylKit data format

Usage

metevalue.methylKit.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

- chr and pos are keys;

- g1~g2: methylation rate data in groups.

input_filename_b

the output file of methylKit. a methylDiff or methylDiffDB object containing the differential methylated locations satisfying the criteria. 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

- strand: Strand

- p: p-value

- qvalue: The adjusted p-value based on BH method

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

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