Filter out pct.2 <0.5

Question

[Chris]

Hi all,

Would you remind me how to filter out pct.2 < 0.5 in this case:

markers %>%
    group_by(cluster) %>% 
    slice_min(n = 2, order_by = avg_log2FC)

I tried filter(markers, markers$pct.2 < 0.5) but I got error.

Thank you so much!

Answer 1

[LChart]

With the %>% syntax in dplyr, you do not need to reference the input variable/table: %>% filter(pct.2 < 0.5) should work.

[Chris]

Thank you so much!

markers <- markers %>%
        group_by(cluster) %>% 
        slice_max(n = 2, order_by = avg_log2FC) %>% filter(pct.2 < 0.5)
En_Vol <- EnhancedVolcano(markers, x = "avg_log2FC", y = "p_val", lab = rownames(markers),
                pCutoff = 1e-4, FCcutoff = 1)

I don't know why after I assigned it back to markers, the volcano plot only has a few dots with numbers, not the gene names as before.