| varevalue.metilene {metevalue} | R Documentation |
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"
)
Arguments
a |
A data.frame object:
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'. |
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
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)