To get frequency within a group:
library(dplyr)
mtcars %>% count(cyl, gear) %>% mutate(Freq = n/sum(n))
# Source: local data frame [8 x 4]
# Groups: cyl [3]
#
# cyl gear n Freq
# (dbl) (dbl) (int) (dbl)
# 1 4 3 1 0.09090909
# 2 4 4 8 0.72727273
# 3 4 5 2 0.18181818
# 4 6 3 2 0.28571429
# 5 6 4 4 0.57142857
# 6 6 5 1 0.14285714
# 7 8 3 12 0.85714286
# 8 8 5 2 0.14285714
or equivalently,
mtcars %>% group_by(cyl, gear) %>% summarise(n = n()) %>% mutate(Freq = n/sum(n))
Careful of what the grouping is at each stage, or your numbers will be off.