Dre_emb_larv | R Documentation |
Transcriptomic data from D. rerio egg to larval samples.
Dre_emb_larv
An object of class list
of length 6.
One time series is included in this dataset.
domazet2010phylogeneticallyzebraRef
The gene expression matrix is log(X + 1)
of quantile-normalized expression data.
A list with :
$g
: The gene expression matrix (genes as rows, samples as columns)
$p
: A dataframe of phenotypic data on the samples, usually :
sname
: The sample names (and colnames of the gene expression matrix).
age
: Sample developmental age. May be scaled to join multiple datasets.
cov
: A factor separating the samples into groups if needed (e.g multiple datasets, batches); else NULL.
age_ini
: Sample chronological age, as given in the literature.
accession
: Sample accession ID for GEO/ArrayExpress.
$geim_params
: A list of elements needed for the gene expression interpolation model :
$formula
: the model formula.
$method
: the model type (eg. gam, glm).
$dim_red
: the dimension reduction method to use (pca, ica).
$nc
: The number PCA/ICA components to use in the model.
$t.unit
: the time series unit (e.g 'hours').
$cov.levels
: a named list of potential covariate with the level to interpolate as.
$metadata
: a named list of extra metadata (e.g organism, profiling technology).
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