metevalue.metilene.chk {metevalue}

Check the Metilene data format

Description

Check the Metilene data format

Usage

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

Arguments

input_filename_a

metilene input file path. 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

metilene input file path. This file should stored as a sep(e.g. TAB) separated file with two key columns and several value columns: 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

- 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

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_metilene_input)
#data(demo_metilene_out)
#example_tempfiles = tempfile(c("metilene_input", "metilene_out"))
#tempdir()
#write.table(demo_metilene_input, file=example_tempfiles[1],
#      row.names=FALSE, col.names=TRUE, quote=FALSE, sep='\t')
#write.table(demo_metilene_out, file=example_tempfiles[2],
#      sep ="\t", row.names =FALSE, col.names =TRUE, quote =FALSE)
#result = metevalue.metilene.chk(example_tempfiles[1], example_tempfiles[2],
#      bheader = TRUE)