cobradata_example_sval: Example data set with three differential gene expression...

In markrobinsonuzh/iCOBRA: Comparison and Visualization of Ranking and Assignment Methods

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.

markrobinsonuzh/iCOBRA documentation built on March 28, 2024, 2:01 p.m.