Summary and relative abundance

[MoemenEltobgy]

I am trying to have some summary stats for all my analytes and also summary for them after grouping according to gender or mortality. I do not know how to use SomaDataIO to do that so I used it in combination with diplyr package.
I have ran into an error while trying to save my summary files and export them as CSV.
Now my questions are:

1. what is the proper way to do these summary stuff I mentioned? if the way i used is valid, then how can i correct this error and export the files?
2. I want also have some relative abundance for all my data and then for the groups I created. If anyone knows how to get this done, it would be a great help.

thanks

Please describe your question with R code if appropriate:

#summ.1<-getAnalytes(my_adat.1)
> summ.gender<-my_adat.1[, summ.1] %>%
+   split(my_adat.1$demo_sex) %>%
+   lapply(summary)
> summ.alive<-my_adat.1[, summ.1] %>%
+   split(my_adat.1$Alive) %>%
+   lapply(summary)
> summ.all<-my_adat.1[, summ.1] %>%
+   lapply(summary)
> write_csv(summ.gender, file = "~/Documents/summarygender.csv")
Error in write_delim(x, file, delim = ",", na = na, append = append, col_names = col_names,  : 
  is.data.frame(x) is not TRUE
> typeof(summ.alive)
[1] "list"
> is.data.frame(summ.alive)
[1] FALSE

Priority Level

• High

---

Thanks for using SomaDataIO!

[stufield]

We have a summary() method for the soma_adat class that will summarize as you describe.
Please see the ?summary.soma_adat help page (and examples therein).

To export the output of the summary() generic, see ?sink or ?dput.

In addition, the example you proved will fail on another user's machine. It is much easier to help you to a solution if the example you provide is executable. Please see the reprex package along with their do's and don'ts.

For example:

mmps <- c("seq.2579.17", "seq.2788.55", "seq.2789.26", "seq.4925.54")
foo <- example_data[, mmps] |> 
  split(example_data$Sex) |>
  lapply(summary)
foo

sink("foo.txt")
foo
sink(NULL)

[stufield]

Alternatively, if you need the export to be a *.csv:

lapply(names(foo), function(x) {
  write.csv(foo[[x]], file = paste0(x, ".csv"), row.names = FALSE, quote = FALSE)
})

[stufield]

Forwarded on to technical support techsupport@somalogic.com