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

In csoneson/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 and estimated absolute 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

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

empty data frame

score

data frame with estimated absolute 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 absolute 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.

csoneson/iCOBRA documentation built on Nov. 5, 2024, 7:20 p.m.