Using dplyr to calculate geomean in a row wise fashion

February 17, 2023

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()

>Solution :

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