simdata: Example RNA-Seq data from paired observations

In ewynn610/corrRNASeq: Model Fitting for Correlated RNA-Seq Count Data

Example RNA-Seq data from paired observations

Description

A list containing 4 components: a data frame that has the sample metadata, a matrix with RNA-Seq counts (simulated from a negative binomial distribution), a matrix with transformed gene expression values, and a vector denoting if each gene in the count/transformed expression matrices is differentially expressed (changes in expression from baseline to follow up in the treatment group).

Usage

simdata

Format

A list with 4 named objects:

metadata

Data frame with variables for group, time, and subject ID. The DESeq2 size factors (log scale) are also included for use as an offset term. Rows are in the same order as columns of counts.

counts

Gene expression values.

vst_expr

Transformed gene expression values using the vst function from the DESeq2-package

de

Vector of logical values denoting if each gene (row) in counts and vst_expr is differentially expressed.

Details

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ewynn610/corrRNASeq documentation built on Sept. 29, 2023, 10:37 a.m.