formatData() function improvement

[julien-roux]

In this function, the expressionSet phenoData are taken from the processed expression values data frame.

Wouldn't it be better to use the annotation retrieved with the getAnnotation() function?

[julien-roux]

In fact, is this function really necessary?

It would be possible to add a format argument to getData() to set the returned format of the data. Possible values:

• As it is now :

   If experimentId is not specified, returns a list of data frames
   with data from all experiments for targeted species and data type.
   If experimentId is specified, returns a data frame with data from
   this experiment.

• We could return an object (or a list of objects) from the SummarizedExperiment class. This is more flexible than the ExpressionSet class because several matrices can be included (TPMs, RPKMs, calls, etc). See https://bioconductor.org/packages/release/bioc/html/SummarizedExperiment.html

• The Bgee data files format (everything in rows, with gene IDs repeated for each sample) fits well into the tidyverse framework, and is in essence very close to the idea of a tibble (https://cran.r-project.org/web/packages/tibble/vignettes/tibble.html). Here is an idea of things you can do if the getData function was returning a tibble:

bgee <- Bgee$new(species = "Mus_musculus", dataType = "rna_seq")
dataMouseGSE30617 <- getData(bgee, experimentId = "GSE30617")
library(dplyr)
as_tibble(dataMouseGSE30617) ## This is a format we could return data into
## Operations on tibble are then easy:
as_tibble(dataMouseGSE30617) %>% select(Gene.ID, Library.ID, TPM) %>% spread(key=Library.ID, value=TPM)