Description Usage Format Source References Examples
A subsample of the RNAseq data from Baduel et al. studying Arabidopsis Arenosa physiology.
1 
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). HabitatAssociated Life History and StressTolerance Variation in Arabidopsis Arenosa. Plant Physiology, 171(1):43751. 10.1104/pp.15.01875.
Agniel D & Hejblum BP (2017). Variance component score test for timecourse gene set analysis of longitudinal RNAseq data, Biostatistics, 18(4):589604. 10.1093/biostatistics/kxx005. arXiv:1605.02351.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22  ## 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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