Subtract a column in a dataframe from many columns in R

Another solution using dplyr::mutate_at() function

# install.packages("dplyr", dependencies = TRUE)
library(dplyr)

df <- data.frame(x = 100:101, y = 2:3, z = 3:4, a = -1:0, b = 4:5)
df %>%
  mutate_at(vars(-matches("y"), -matches("x")), list(dif = ~ . - y))
#>     x y z  a b z_dif a_dif b_dif
#> 1 100 2 3 -1 4     1    -3     2
#> 2 101 3 4  0 5     1    -3     2

^{Created on 2019-11-05 by the reprex package (v0.3.0)}

If you need to subtract the columns 3:ncol(df) from the second column

df[3:ncol(df)] <- df[3:ncol(df)]-df[,2]