baduel_5gs: Small portion of RNA-seq data from plant physiology study.

In dearseq: Differential Expression Analysis for RNA-seq data through a robust variance component test

Description

A subsample of the RNA-seq data from Baduel et al. studying Arabidopsis Arenosa physiology.

Usage

data(baduel_5gs)

Format

3 objects

• design: a design matrix for the 48 measured samples, containing the following variables:

  • SampleName corresponding column names from expr_norm_corr

  • Intercept an intercept variable

  • Population a factor identifying the plant population

  • Age_weeks numeric age of the plant at sampling time (in weeks)

  • Replicate a purely technical variable as replicates are not from the same individual over weeks. Should not be used in analysis.

  • Vernalized a logical variable indicating whether the plant had undergone vernalization (exposition to cold and short day photoperiods)

  • Vernalized a binary variable indicating whether the plant belonged to the KA population

  • AgeWeeks_Population interaction variable between the AgeWeeks and Population variables

  • AgeWeeks_Vernalized interaction variable between the AgeWeeks and Vernalized variables

  • Vernalized_Population interaction variable between the Vernalized and Population variables

  • AgeWeeks_Vernalized_Population interaction variable between the AgeWeeks, Vernalized and Population variables

• baduel_gmt: a gmt object containing 5 gene sets of interest (see GSA.read.gmt), which is simply a list with the 3 following components:

  • genesets: a list of n gene identifiers vectors composing eachgene set (each gene set is represented as the vector of the gene identifiers composing it)

  • geneset.names: a vector of length n containing the gene set names (i.e. gene sets identifiers)

  • geneset.descriptions: a vector of length n containing gene set descriptions (e.g. textual information on their biological function)

• expr_norm_corr: a numeric matrix containing the normalized batch corrected expression for the 2454 genes included in either of the 5 gene sets of interests

Source

http://www.ncbi.nlm.nih.gov/bioproject/PRJNA312410

References

Baduel P, Arnold B, Weisman CM, Hunter B & Bomblies K (2016). Habitat-Associated Life History and Stress-Tolerance Variation in Arabidopsis Arenosa. Plant Physiology, 171(1):437-51. 10.1104/pp.15.01875.

Agniel D & Hejblum BP (2017). Variance component score test for time-course gene set analysis of longitudinal RNA-seq data, Biostatistics, 18(4):589-604. 10.1093/biostatistics/kxx005. arXiv:1605.02351.

Examples

if(interactive()){
data('baduel_5gs')

set.seed(54321)
KAvsTBG <- dgsa_seq(exprmat=log2(expr_norm_corr+1),
                    covariates=apply(as.matrix(design[,
  c('Intercept', 'Vernalized', 'AgeWeeks', 'Vernalized_Population',
  'AgeWeeks_Population'), drop=FALSE]), 2, as.numeric),
                     variables2test =
                         as.matrix(design[, c('PopulationKA'), drop=FALSE]),
                     genesets=baduel_gmt$genesets[c(3,5)],
                     which_test = 'permutation', which_weights = 'loclin',
                     n_perm=1000, preprocessed = TRUE)

set.seed(54321)
Cold <- dgsa_seq(exprmat=log2(expr_norm_corr+1),
                 covariates=apply(as.matrix(design[,
   c('Intercept', 'AgeWeeks', 'PopulationKA', 'AgeWeeks_Population'),
   drop=FALSE]), 2, as.numeric),
                variables2test=as.matrix(design[, c('Vernalized',
                 'Vernalized_Population')]),
                 genesets=baduel_gmt$genesets[c(3,5)],
                 which_test = 'permutation', which_weights = 'loclin',
                 n_perm=1000, preprocessed = TRUE)
}

dearseq documentation built on Nov. 8, 2020, 5:49 p.m.