Mm.phenomat


The phenotype matrix <code>Mm.phenomat</code> contains information about the experimental design. It is comprised of the filename, the type of RNA fraction measured (T, U or L), the labeling time and the replicate number.


datasets

Dynamic Transcriptome Analysis (DTA) can monitor the cellular response to perturbations with higher sensitivity and temporal resolution than standard transcriptomics. The package implements the underlying kinetic modeling approach capable of the precise determination of synthesis- and decay rates from individual microarray or RNAseq measurements.

Bjoern Schwalb

Dynamic Transcriptome Analysis

Mm.phenomat function

The phenomat is a matrix comprised of the file name, the type of RNA fraction mesasured (T, U or L, <code>fraction</code> column), the labeling time (<code>time</code>,<code>timeframe</code> column) and the replicate number (<code>nr</code> column). Rows in this matrix represent the individual experiments.

Format

Doelken, L., Ruzsics, Z., Raedle, B., Friedel, C. C., Zimmer, R., Mages, J., Hoffmann, R., Dickinson, P., Forster, T., Ghazal, P., & Koszinowski, U. H. (2008). High-resolution gene expression profiling for simultaneous kinetic parameter analysis of RNA synthesis and decay. RNA 14(9), 1959-1972.

Source

The phenotype matrix <code>Mm.phenomat</code> contains information about the experimental design. It is comprised of the filename, the type of RNA fraction measured (T, U or L), the labeling time and the replicate number.

Mm.phenomat: Design of the Mus Musculus DTA experiment from Doelken et al.

Description

Usage

Arguments

Format

Source