Wilcoxon test for methylation data

Get p.value from Wilcoxon test based on methylation rate in two probes. This function doesn't respect tiles or tiles.common column. This function is using in find_DMR and can be used sepparately.

test_wilcoxon(data)

Arguments

data	There are two options: 1. dataframe with specific columns: chr, poz, prob, no, meth, unmeth, meth.rate. This dataframe is result of function preprocessing. 2. dataframe with specific columns: chr, poz, prob, no, meth, unmeth, meth.rate, tiles and possible tiles.common columns. This dataframe is result of function create_tiles_min_gap or create_tiles_fixed_length.

Value

p.value from Wilcoxon test or na values if something goes wrong

Examples

data('schizophrenia')
control <- schizophrenia %>% filter(category == 'control') %>%
dplyr::select(-category)

disease <- schizophrenia %>% filter(category == 'disease') %>%
 dplyr::select(-category)

data <- preprocessing(control, disease)
data.tiles <- create_tiles_max_gap(data, gaps.length = 100)
data.test <- data.tiles %>% filter(tiles == 10)
test_wilcoxon(data.test)
#> Warning: cannot compute exact p-value with ties
#>     p.value
#> 1 0.1735682
# or by some self-defined regions:
data.test.2 <- data.tiles %>% filter(chr == 'chr1', poz > 80000, poz < 100000)
test_wilcoxon(data.test.2)
#>        p.value
#> 1 7.480529e-11