baduel_5gs | R Documentation |
A subsample of the RNA-seq data from Baduel et al. studying Arabidopsis Arenosa physiology.
data(baduel_5gs)
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
)
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
https://www.ncbi.nlm.nih.gov/bioproject/PRJNA312410/
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. doi: 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. doi: 10.1093/biostatistics/kxx005. arXiv:1605.02351.
## Not run: rm(list=ls()) data("baduel_5gs") set.seed(54321) KAvsTBG <- tcgsa_seq(y=log2(expr_norm_corr+1), x=apply(as.matrix(design[, c("Intercept", "Vernalized", "Age_weeks", "Vernalized_Population", "AgeWeeks_Population"), drop=FALSE]), 2, as.numeric), phi=as.matrix(design[, c("PopulationKA"), drop=FALSE]), genesets=baduel_gmt$genesets[c(3,5)], which_test = "permutation", which_weights = "loclin", n_perm=1000, preprocessed = TRUE, doPlot = TRUE) set.seed(54321) Cold <- tcgsa_seq(y=log2(expr_norm_corr+1), x=apply(as.matrix(design[, c("Intercept", "Age_weeks", "PopulationKA", "AgeWeeks_Population"), drop=FALSE]), 2, as.numeric), phi=as.matrix(design[, c("Vernalized", "Vernalized_Population")]), genesets=baduel_gmt$genesets[c(3,5)], which_test = "permutation", which_weights = "loclin", n_perm=1000, preprocessed = TRUE, doPlot = TRUE) ## End(Not run)
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