Dre_emb_larv: Dre_emb_larv

In LBMC/zebraRef: Zebrafish Reference Data For The RAPToR Package

Dre_emb_larv

Description

Transcriptomic data from D. rerio egg to larval samples.

Usage

Dre_emb_larv

Format

An object of class list of length 6.

Details

One time series is included in this dataset.

• \insertCite

  domazet2010phylogeneticallyzebraRef

The gene expression matrix is log(X + 1) of quantile-normalized expression data.

Format

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).

Source

GSE24616

References

\insertAllCited

LBMC/zebraRef documentation built on April 7, 2023, 7:27 a.m.