metevalue.biseq.chk {metevalue}

Check the BiSeq data format

Description

Check the BiSeq data format

Usage

metevalue.biseq.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

- 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 site of the corresponding region

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

- range: The range of the corresponding region

- strand: Strand

- median.p: The median of p-values in the corresponding region

- median.meth.group1 : The median of methylation level for the corresponding segment of group 1

- median.meth.group2 : The median of methylation level for the corresponding segment of group 2

- median.meth.diff: The median of the difference between the 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_biseq_methyrate")
#data("demo_biseq_DMR")
#example_tempfiles = tempfile(c("demo_biseq_methyrate", "demo_biseq_DMR"))
#tempdir()
#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.chk(example_tempfiles[1],
#                         example_tempfiles[2], bheader = TRUE)