Creating a column with factor variables conditional on multiple other columns? - r

Question

I have 4 columns, called Amplification, CNV.gain, Homozygous.Deletion.Frequency, Heterozygous.Deletion.Frequency. I want to create a new column in which, if any of the values in these 4 columns are:
greater than or equal to 5 and less than or equal to 10, it returns low:
greater than 10 and less than or equal to 20, it returns medium
greater than 20, it returns high
An example of the final table (long_fused) would look like this:
CNV.Gain
Amplification
Homozygous.Deletion.Frequency
Heterozygous.Deletion.Frequency
Threshold
3
5
10
0
Low
0
0
11
8
Medium
7
16
25
0
High
So far, I've tried the following code, although it seems to fill in the "Threshold" Column, is doing so incorrectly.
library(dplyr)
long_fused <- long_fused %>%
mutate(Percent_sample_altered = case_when(
Amplification>=5 & Amplification < 10 & CNV.gain>=5 & CNV.gain < 10 | CNV.gain>=5 & CNV.gain<=10 & Homozygous.Deletion.Frequency>=5 & Homozygous.Deletion.Frequency<=10| Heterozygous.Deletion.Frequency>=5 & Heterozygous.Deletion.Frequency<=10 ~ 'Low',
Amplification>= 10 & Amplification<20 |CNV.gain>=10 & CNV.gain<20| Homozygous.Deletion.Frequency>= 10 & Homozygous.Deletion.Frequency<20 | Heterozygous.Deletion.Frequency>=10 & Heterozygous.Deletion.Frequency<20 ~ 'Medium',
Amplification>20 | CNV.gain >20 | Homozygous.Deletion.Frequency >20 | Heterozygous.Deletion.Frequency>20 ~ 'High'))
As always any help is appreciated!
Data in dput format
long_fused <-
structure(list(CNV.Gain = c(3L, 0L, 7L), Amplification = c(5L,
0L, 16L), Homozygous.Deletion.Frequency = c(10L, 11L, 25L),
Heterozygous.Deletion.Frequency = c(0L, 8L, 0L), Threshold =
c("Low", "Medium", "High")), class = "data.frame",
row.names = c(NA, -3L))

Answer 1

Here is a way with rowwise followed by base function cut.
library(dplyr)
long_fused %>%
rowwise() %>%
mutate(new = max(c_across(-Threshold)),
new = cut(new, c(5, 10, 20, Inf), labels = c("Low", "Medium", "High"), left.open = TRUE))

Answer 2

Here's an alternative using case_when -
library(dplyr)
long_fused %>%
mutate(max = do.call(pmax, select(., -Threshold)),
#If you don't have Threshold column in your data just use .
#mutate(max = do.call(pmax, .),
Threshold = case_when(between(max, 5, 10) ~ 'Low',
between(max, 11, 15) ~ 'Medium',
TRUE ~ 'High'))
# CNV.Gain Amplification Homozygous.Deletion.Frequency
#1 3 5 10
#2 0 0 11
#3 7 16 25
# Heterozygous.Deletion.Frequency max Threshold
#1 0 10 Low
#2 8 11 Medium
#3 0 25 High