Sc.phenomat.dynamic


The phenotype matrix <code>Sc.phenomat.dynamic</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, the replicate number and an additional number indicating the timecourse order.


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

Sc.phenomat.dynamic 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), the replicate number (<code>nr</code> column) and a number indicating the timecourse order (<code>timecourse</code> column). Rows in this matrix represent the individual experiments.

Format

C. Miller, B. Schwalb, K. Maier, D. Schulz, S. Duemcke, B. Zacher, A. Mayer, J. Sydow, L. Marcinowski, L. Doelken, D. E. Martin, A. Tresch, and P. Cramer. Dynamic transcriptome analysis measures rates of mRNA synthesis and decay in yeast. Mol Syst Biol, 7:458, 2011.

Source

The phenotype matrix <code>Sc.phenomat.dynamic</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, the replicate number and an additional number indicating the timecourse order.

Sc.phenomat.dynamic: Design of the Saccharomyces Cerevisiae salt stress DTA experiment from Miller et al.

Description

Usage

Arguments

Format

Source