diff --git a/omics/week-5/workshop.qmd b/omics/week-5/workshop.qmd index 26278fe..af95501 100644 --- a/omics/week-5/workshop.qmd +++ b/omics/week-5/workshop.qmd @@ -110,9 +110,8 @@ s30_results <- read_csv("results/S30_results.csv") the dataframes (perhaps using `glimpse()`) ```{r} +#| include: false #---CODING ANSWER--- -#| echo: false -#| output: false glimpse(s30_count_norm) ``` @@ -135,9 +134,8 @@ glimpse(s30_count_norm) ```{r} +#| include: false #---CODING ANSWER--- -#| echo: false -#| output: false glimpse(s30_results) ``` @@ -293,9 +291,8 @@ s30_results_sig0.01 <- s30_results |> 🎬 Write the dataframe to file ```{r} +#| include: false #---CODING ANSWER--- -#| echo: false -#| output: false # write to csv file write_csv(s30_results_sig0.01, file = "results/s30_results_sig0.01.csv") @@ -305,9 +302,8 @@ write_csv(s30_results_sig0.01, write to file: ```{r} +#| include: false #---CODING ANSWER--- -#| echo: false -#| output: false s30_results_sig0.05 <- s30_results |> filter(padj <= 0.05) @@ -560,7 +556,7 @@ interpretation. the names `prog` and `hspc` for the dataframes. ```{r} -#| echo: false +#| include: false #---CODING ANSWER--- # import the normalised counts prog <- read_csv("data-raw/surfaceome_prog.csv") @@ -580,7 +576,7 @@ prog_hspc <- bind_cols(prog, hspc[-1]) used the name `prog_hspc_results` for the dataframe. ```{r} -#| echo: false +#| include: false #---CODING ANSWER--- # import the DE results prog_hspc_results <- read_csv("results/prog_hspc_results.csv") @@ -590,9 +586,8 @@ prog_hspc_results <- read_csv("results/prog_hspc_results.csv") the dataframes (perhaps using `glimpse()`) ```{r} +#| include: false #---CODING ANSWER--- -#| echo: false -#| output: false glimpse(prog_hspc) ``` @@ -601,9 +596,8 @@ glimpse(prog_hspc) ```{r} +#| include: false #---CODING ANSWER--- -#| echo: false -#| output: false glimpse(prog_hspc_results) ``` @@ -688,8 +682,7 @@ Oh, **`conflicted`** has flagged a conflict for us. ```{r} -#| echo: false -#| output: false +#| include: false #---CODING ANSWER--- prog_hspc_results |> dplyr::select(ensembl_gene_id) |> filter(!ensembl_gene_id %in% gene_info$ensembl_gene_id) @@ -729,19 +722,16 @@ prog_hspc_results_sig0.01 <- prog_hspc_results |> 🎬 Write the dataframe to file ```{r} +#| include: false #---CODING ANSWER--- -#| echo: false -#| output: false write_csv(prog_hspc_results_sig0.01, file = "results/prog_hspc_results_sig0.01.csv") ``` 🎬 Create a dataframe of the genes significant at the 0.05 level and write to file: ```{r} +#| include: false #---CODING ANSWER--- -#| echo: false -#| output: false - prog_hspc_results_sig0.05 <- prog_hspc_results |> filter(FDR <= 0.05)