curated_expressiondata {SMITE} | R Documentation

## A toy dataset ofcurated RNA-seq to test within SMITE

### 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)

[Package SMITE version 1.8.0 Index]