bootEWAS.RdUsers can perform internal validation of the identified differently methylated sites based on the bootstrap method.
bootEWAS(input, filterP = "PVAL", cutoff = 0.05, CpGs = NULL, times = 500,
bootCI = "perc",filename = "default")An R6 class integrated with all the information obtained from the startEWAS or plotEWAS function.
The name of the p value columns such as "PVAL", "FDR", and "Bonfferoni." Users use this P-value to screen for significance sites and further conduct internal validation.
The cutoff value of the P-value used to filter for further internal validation. The default is 0.05.
The name of the methylation site specified by the user for bootstrap analysis, separated by commas. Be careful not to have spaces, such as "cpg1,cpg2".
Number of bootstrap times specified by the user. The default value is 100 times.
A vector of character strings representing the type of interval to base the test on. The value should be one of "norm", "basic", "stud", "perc" (the default), and "bca".
User-customized .csv file name for storing bootstrap results. If "default", it will be named as "bootresult".
input, An R6 class object integrating all information.
if (FALSE) { # \dontrun{
res <- initEWAS(outpath = "default")
res <- loadEWAS(input = res, ExpoData = "default", MethyData = "default")
res <- transEWAS(input = res, Vars = "cov1", TypeTo = "factor")
res <- startEWAS(input = res, chipType = "EPICV2", model = "lm", expo = "default", adjustP = TRUE)
res <- bootEWAS(input = res, filterP = "PVAL", cutoff = 0.05, times = 100)
} # }