How to work with dplyr verbs in the colData slot of SingleCellExperiment objects?
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ramonmassoni ▴ 10
@ramonmassoni-19642
Last seen 2.6 years ago

Hi,

I'm trying to work in a tidyverse framework with the cell metadata (colData) of a SingleCellExperiment object. To do that, I have to explicitly convert it to a data frame with (as.data.frame). However, if I try to set colData(sce) <- as.data.frame(colData(sce)), it throws an error. I tried to convert it to a datatable with (as.data.table), but it didn't work either. If you have any insight it would be much appreciate it, especially since dplyr is one of the most useful packages to work with standard data frames.

Thanks,

Ramon

SingleCellExperiment • 845 views
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@martin-morgan-1513
Last seen 3 days ago
United States

These S4 objects are based on 'DataFrame', so

> colData(sce) = as(colData(sce), "DataFrame")

Or

> colData(sce) = colData(sce) %>% as.data.frame() %>% etc... %>% DataFrame()
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