transcriptome

<p>A count table of a highly replicated RNA-seq experiment
with samples by column and genes by row. Two groups composed
of SNF2 knockout and WT, 48 samples in each.</p>

datasets

A set of tests for compositional pathologies. Tests for coherence of correlations with aIc.coherent() as suggested by (Erb et al. (2020) <doi:10.1016/j.acags.2020.100026>),  compositional dominance of distance with aIc.dominant(), compositional perturbation invariance with aIc.perturb() as suggested by (Aitchison (1992) <doi:10.1007/BF00891269>) and singularity of the covariation matrix with aIc.singular(). Currently tests five data transformations: prop, clr, TMM, TMMwsp, and RLE from the R packages 'ALDEx2', 'edgeR' and 'DESeq2' (Fernandes et al (2014) <doi:10.1186/2049-2618-2-15>, Anders et al. (2013)<doi:10.1038/nprot.2013.099>).

Greg Gloor

Testing for Compositional Pathologies in Datasets

transcriptome function

<p>A data frame with 96 columns and 5892 rows</p>

transcriptome: Saccharomyces cerevisiae transcriptome

Description

Usage

Arguments

Format