ttest_data: applying t-test analysis

In ABC.RAP: Array Based CpG Region Analysis Pipeline

Description

This function applies "two.sided", unequal variance Student's t-test analysis for each probe comparing cases and controls. A cutoff for p-values can be entered to minimise multiple testing bias to filter insignificant p-values.

Usage

ttest_data(x, cases_column_1, cases_column_n, controls_column_1,
  controls_column_n, ttest_cutoff)

Arguments

x	The filtered 450k probes from filter_data() function
cases_column_1	The first column (column number) for cases in the filtered dataset
cases_column_n	The last column (column number) for cases in the filtered dataset
controls_column_1	The first column (column number) for controls in the filtered dataset
controls_column_n	The last column (column number) for controls in the filtered dataset
ttest_cutoff	The cutoff level to filter insignificant p-values

Examples

data(test_data)
data(nonspecific_probes)
test_data_filtered <- filter_data(test_data)
test_data_ttest <- ttest_data(test_data_filtered, 1, 2, 3, 4, 1e-3)

ABC.RAP documentation built on May 2, 2019, 9:16 a.m.