metevalue.DMRfinder {metevalue} | R Documentation |
Calculate E-value of the DMRfinder data format
Description
Calculate E-value of the DMRfinder data format
Usage
metevalue.DMRfinder(
methyrate,
DMRfinder.output,
adjust.methods = "BH",
sep = "\t",
bheader = FALSE
)
Arguments
methyrate |
is the methyrate file. For example:
The columns are (in order): - chr: Chromosome - pos: int Position - g1~g2: methylation rate data in groups | |||||||||||||||||
DMRfinder.output |
is the output file of DMRfinder. - chr: Chromosome - start: The positions of the start sites of the corresponding region - end: The positions of the end sites of the corresponding region - CpG: The number of CpG sites within the corresponding region - Control.mu: The average methylation rate in control group - Expt1.mu: The average methylation rate in experiment group - Control.Expt1.diff: The methylation difference between control and experiment groups - Control.Expt1.pval: P-value based on Wald-test. | |||||||||||||||||
adjust.methods |
is the adjust methods of e-value. It can be 'bonferroni', 'hochberg', 'holm', 'hommel', 'BH', 'BY' | |||||||||||||||||
sep |
seperator, default is the TAB key. | |||||||||||||||||
bheader |
a logical value indicating whether the DMRfinder.output file contains the names of the variables as its first line. By default, bheader = FALSE. |
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_DMRfinder_rate_combine)
data(demo_DMRfinder_DMRs)
#example_tempfiles = tempfile(c("rate_combine", "DMRfinder_out"))
#tempdir()
#write.table(demo_DMRfinder_rate_combine, file=example_tempfiles[1],
# row.names=FALSE, col.names=TRUE, quote=FALSE, sep='\t')
#write.table(demo_DMRfinder_DMRs, file=example_tempfiles[2],
# sep ="\t", row.names =FALSE, col.names =TRUE, quote =FALSE)
#result = metevalue._DMRfinder(example_tempfiles[1], example_tempfiles[2],
# bheader = TRUE)
#head(result)