methylationdata: A toy dataset of DNA methylation to test within SMITE

In AJEinstein/SMITE: Significance-based Modules Integrating the Transcriptome and Epigenome

Description

A toy dataset of raw DNA methylation from HELP-tagging. The file is a BED file with columns added for effect and p-value.

Usage

data(methylationdata)

Format

A data frame with 40000 observations on the following 5 variables.

column1

a character vector specifying chromsome

column2

an integer vector specifying start

column3

an integer vector specifying end

column4

a numeric vector with an effect direction (here it is average difference between two groups)

column5

a numeric vector with a two sided t-test p-value

Details

This is a small subset of a DNA methylation dataset is a randomized version of the Toxoplasma dataset used to benchmark. We could not include the larger version do to package size requirements but larger versions are available. See Github source below. It still has NAs and p-values=0.

Value

A dataframe in BED format (chromosome, start, end) with additional columns for and effect direction and p-value derived from T-tests of HELP-tagging DNA methylation data.

Source

Manuscript in preparation. Please see https://github.com/GreallyLab/SMITE for more details.

Examples

data(methylationdata)

any(is.na(methylation[, 4]))

any(methylation[, 4] == 0)

AJEinstein/SMITE documentation built on Oct. 23, 2021, 7:44 a.m.