curated_expression: A toy dataset ofcurated RNA-seq to test within SMITE

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

Description

A toy dataset of pre-cleaned gene expression data from RNA-seq. The file is effect and p-value with gene names as rownames.

Usage

data("curated_expressiondata")

Format

A data frame with 20819 observations on the following 2 variables.

rownames

a character vector specifying gene

column1

an numeric vector specifying effect (log fold change)

column2

a numeric vector with a two sided p-value from DESeq analysis

Details

This gene expression dataset is a randomized version of the Toxoplasma dataset used to benchmark SMITE. It no longer has NAs or p-values=0. Gene names were converted to gene symbols.

Value

A dataframe with rownames as genes in Refseq format and columns for effects and pvalues derived from negative binomial testing of DESeq normalized values from RNA-seq.

Source

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

Examples

data(curated_expressiondata)

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