I'd like to calculate the geomean using each row from three columns. I found solutions to calculate it from the values in one column (example), but not from a row.
Here's a simplified example:
data <- structure(list(fs_id = structure(1:8, levels = c("CON1", "NC",
"water", "SCR1", "FAN1_1", "CON2", "SCR2", "FAN1_2"), class = "factor"),
twodct_ATP5B = c(1.06960527260684, 0.00241424406360917, NA,
0.953100847649869, 0.404512354245938, 0.934924336678708,
1.32283164360403, 0.194667767059346), twodct_EIF4A2 = c(1.07741209897215,
NA, NA, 1.01873805854745, 0.467988708062081, 0.928149963188649,
1.31762036152893, 0.33377442013251), twodct_GAPDH = c(1.04388739915294,
0.000156497290441042, NA, 0.972431569982792, 0.547030142788418,
0.957957726869246, 0.942311505534324, 0.337842927620691)), row.names = c(NA,
-8L), class = c("tbl_df", "tbl", "data.frame"))
The table looks like this:
> data
# A tibble: 8 × 4
fs_id twodct_ATP5B twodct_EIF4A2 twodct_GAPDH
<fct> <dbl> <dbl> <dbl>
1 CON1 1.07 1.08 1.04
2 NC 0.00241 NA 0.000156
3 water NA NA NA
4 SCR1 0.953 1.02 0.972
5 FAN1_1 0.405 0.468 0.547
6 CON2 0.935 0.928 0.958
7 SCR2 1.32 1.32 0.942
8 FAN1_2 0.195 0.334 0.338
I want to get the row wise geomean of columns twodct_ATP5B, twodct_EIF4A2 and twodct_GAPDH.
I've had a crack like this, but doesn't seem to work:
data %>%
rowwise() %>%
dplyr::mutate(geomean = exp(mean(log(select(., c("twodct_ATP5B", "twodct_EIF4A2", "twodct_GAPDH")))))) %>%
ungroup()
This is a good time to use c_across within the rowwise:
data %>%
rowwise() %>%
dplyr::mutate(geomean = exp(mean(log(c_across(c(twodct_ATP5B, twodct_EIF4A2, twodct_GAPDH)))))) %>%
ungroup()
# # A tibble: 8 × 5
# fs_id twodct_ATP5B twodct_EIF4A2 twodct_GAPDH geomean
# <fct> <dbl> <dbl> <dbl> <dbl>
# 1 CON1 1.07 1.08 1.04 1.06
# 2 NC 0.00241 NA 0.000156 NA
# 3 water NA NA NA NA
# 4 SCR1 0.953 1.02 0.972 0.981
# 5 FAN1_1 0.405 0.468 0.547 0.470
# 6 CON2 0.935 0.928 0.958 0.940
# 7 SCR2 1.32 1.32 0.942 1.18
# 8 FAN1_2 0.195 0.334 0.338 0.280