cobradata_example_sval {iCOBRA} | R Documentation

## Example data set with three differential gene expression methods

### Description

A data set consisting of p-values, adjusted p-values, s-values and estimated log fold changes (in the 'scores' slot) obtained by three methods for differential expression analysis of RNA-seq data, applied to a small synthetic data set of 3,858 human genes. The values are stored in a `COBRAData` object together with a 'truth' data frame containing the true differential expression status for each gene as well as various additional annotations such as the true log fold change, the number of isoforms of the gene and the average expression level.

### Usage

    cobradata_example_sval

### Format

A `COBRAData` object with five slots:

pval

  data frame with p-values for 2,399 genes, from three different methods.

padj

  data frame with adjusted p-values for 2,399 genes, from two different methods.

sval

  data frame representing s-values for 2,399 genes, from two different methods. Since the purpose of this data set is only to demonstrate functionality, the s-values were obtained by copying the adjusted p-value slot, and thus these values do not represent true s-values.

score

  data frame with estimated log fold changes for 2,399 genes, from three different methods.

truth

  data frame with true differential expression status (status column), the number of isoforms (n_isoforms column), the true log fold change (logFC and logFC_cat columns) and average expression level (expr and expr_cat columns) for 3,858 genes.

### Value

A `COBRAData` object.

[Package iCOBRA version 1.10.0 Index]