metevalue (version 0.2.4)

varevalue.metilene: Calculate E-value of the Metilene data

Description

The data file could be pre-handled by the evalue.metilene.chk function.

Usage

varevalue.metilene(
  a,
  b,
  a_b,
  group1_name = "g1",
  group2_name = "g2",
  adjust.methods = "BH"
)

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

Arguments

a

A data.frame object:

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

i.e two key columns (chrom, pos) with several value columns in groups.

b

A data.frame object stores the data, 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

a_b

A data.frame object of a join b with particular data clean processes. Check the function [evalue.methylKit.chk()] for more details.

group1_name

charactor: The name of the first group. For example, "g1" in the above example.

group2_name

charactor: The name of the second group. For example, "g2" in the above example.

adjust.methods

is the adjust methods of e-value. It can be 'bonferroni', 'hochberg', 'holm', 'hommel', 'BH', 'BY'. The default value is 'BH'.

Examples

#data(demo_metilene_input)
#data(demo_metilene_out)
#result = evalue_buildin_var_fmt_nm(demo_metilene_input, demo_metilene_out, method="metilene")
#result = list(a = result$a, 
#              b = result$b, 
#              a_b = evalue_buildin_sql(result$a, result$b, method="metilene"))
#result = varevalue.metilene(result$a, result$b, result$a_b)