diff --git a/omics/week-4/workshop.qmd b/omics/week-4/workshop.qmd index cc7c512..830911f 100644 --- a/omics/week-4/workshop.qmd +++ b/omics/week-4/workshop.qmd @@ -523,6 +523,8 @@ prog_hspc |> ``` +Notice that we have summed across all the columns. + ❓ What do you conclude? @@ -552,7 +554,7 @@ rowSums(prog_hspc) |> sort() |> head(10) To find the genes that are expressed in only one cell type, we can use the same approach as above but only sum the columns for one cell type. -🎬 Find the genes that are 0 in every column for the Prog cells: +🎬 Find the genes that are 0 in every column for the HSPC cells: ```{r} prog_hspc |> @@ -561,18 +563,21 @@ prog_hspc |> ``` +We have summed across the HSPC cells only. Note that if we knew there were some rows that were all zero across both -cerll types, we would need to add +cell types, we would need to add `|> filter(sum(c_across(Prog_001:Prog_852)) != 0)` -🎬 Now you find the genes that are 0 in every column for the HSPC cells: +meaning zero in all the HSPC but not zero in all the Prog + +🎬 Now you find the genes that are 0 in every column for the Prog cells: ```{r} #| echo: false #---CODING ANSWER--- prog_hspc |> rowwise() |> - filter(sum(c_across(HSPC_001:HSPC_852)) == 0) + filter(sum(c_across(Prog_001:Prog_852)) == 0) ``` @@ -694,7 +699,7 @@ practical. Qmd stands for Quarto markdown. It allows code and ordinary text to be interleaved to produce well-formatted reports including webpages. Right-click on the link and choose Save-As to download. You will be able to open the Qmd file in RStudio. Alternatively, [View in -Browser](https://github.com/3mmaRand/BIO00088H-data/blob/main/omics/week-3/workshop.qmd). Coding and thinking answers are +Browser](https://github.com/3mmaRand/BIO00088H-data/blob/main/omics/week-4/workshop.qmd). Coding and thinking answers are marked with `#---CODING ANSWER---` and `#---THINKING ANSWER---` Pages made with R [@R-core], Quarto [@allaire2022], `knitr` [@knitr],