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UCLouvain-CBIO / scp

Single cell proteomics data processing
https://uclouvain-cbio.github.io/scp/index.html
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vignette: show results #10

Closed lgatto closed 4 years ago

lgatto commented 4 years ago

I think it would be useful to show the results in several code chunks. For example in 

scp <-aggregateFeaturesOverAssays(scp,
                                  i = 1:3,
                                  fcol = "peptide",
                                  name = paste0("peptides_", names(scp)),
                                  fun = matrixStats::colMedians, na.rm = TRUE)

it would be useful to show that the new scp object now has 6 assays. It would help with the next code chunk also, where suddenly you use assays 4 to 6:

scp <- joinAssays(scp,
                  i = 4:6,
                  name = "peptides")
#> harmonizing input:
#>   removing 48 sampleMap rows not in names(experiments)

And again, here, show that there's a new 7th assay called peptides.

cvanderaa commented 4 years ago

Thanks for the comment, I have added a few additional paragraphs and code chunks to clarify the output of some of the functions.