test_ks: Kolmogorov-Smirnov test for methylation data

In geneticsMiNIng/metR: Tools for Identification and Visualisation of Differentially Methylated Regions

Description

Get p.value from K-S 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 separately.

Usage

test_ks(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 K-S 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_ks(data.test)
# or by some self-defined regions:
data.test.2 <- data.tiles %>% filter(chr == 'chr1', poz > 80000, poz < 100000)
test_ks(data.test.2)

geneticsMiNIng/metR documentation built on May 28, 2019, 8:41 p.m.