Conditionals in R

Question

I am not sure how to make this work?

I wish to make a new column in a dataframe dependent on whether or not two other columns meet the following criteria:

if df$Cn_LCIS and df$Cn_ILC are both greater than '2' print '0'

if df$CN_LCIS and df$Cn_ILC are both smaller than '2' print '0'

and if they are the same also print '0' else print '1'

df

        Chromosome     Start       End Cn_ILC mCn_ILC Cn_LCIS mCn_LCIS both
chr1.1        chr1         0  11194349      2       1       2        1    0
chr1.2        chr1 102809740 104579163      2       1       3        1    1
chr1.3        chr1 104579163 121311799      2       1       2        1    0
chr1.4        chr1  11194349  11492125      2       1       3        1    1
chr1.5        chr1  11492125  71442329      2       1       2        1    0
chr1.6        chr1 144009053 157140292      1       1       1        1    0
chr1.7        chr1 157140292 243709339      2       1       1        1    0
chr1.8        chr1 243709339 244112662      3       1       3        1    0
chr1.9        chr1 244112662 249250621      3       1       3        1    0
chr1.10       chr1  71442329  72624878      2       1       3        1    1
chr1.11       chr1  72624878 102809740      2       1       4        1    1

Not working:

df$both <- ifelse(df$Cn_LCIS > 2 & df$Cn_ILC > 2, 0, ifelse (df$Cn_LCIS < 2 & df$Cn_ILC < 2, 0, ifelse (df$Cn_LCIS == 2 & df$Cn_LCIS == 2, 0, ifelse(df$Cn_ILC!=df$Cn_LCIS,1))))

as for ifelse, have a look here: http://stackoverflow.com/questions/16275149/does-ifelse-really-calculate-both-of-its-vectors-every-time-is-it-slow/16275201 — Ricardo Saporta, Sep 29 '14 at 20:27

score 2 · Answer 1 · answered Sep 29 '14 at 20:23

compareTo2 <- function(LCIS, ILC) {
  as.numeric(!((LCIS > 2 & ILC > 2) | (LCIS < 2 & ILC < 2) | (LCIS == ILC) )) 
}

compareTo2(df$Cn_LCIS, df$Cn_ILC)
 # [1] 0 1 0 1 0 0 1 0 0 1 1

If your data is large, you might want to try the following

library(data.table)

DT <- as.data.table(df)

## different syntax for data.table than data.frame
DT[, as.numeric(!((Cn_LCIS > 2 & Cn_ILC > 2) | (Cn_LCIS < 2 & Cn_ILC < 2) | (Cn_LCIS == Cn_ILC) )) ]

## ... or you can assign it as a column
DT[, compare_LCIS_ILC := as.numeric(!((Cn_LCIS > 2 & Cn_ILC > 2) | (Cn_LCIS < 2 & Cn_ILC < 2) | (Cn_LCIS == Cn_ILC) )) ]
DT
#         Chromosome     Start       End Cn_ILC mCn_ILC Cn_LCIS mCn_LCIS both compare_LCIS_ILC
#  1:       chr1         0  11194349      2       1       2        1    0                0
#  2:       chr1 102809740 104579163      2       1       3        1    1                1
#  3:       chr1 104579163 121311799      2       1       2        1    0                0
#  4:       chr1  11194349  11492125      2       1       3        1    1                1
#  5:       chr1  11492125  71442329      2       1       2        1    0                0
#  6:       chr1 144009053 157140292      1       1       1        1    0                0
#  7:       chr1 157140292 243709339      2       1       1        1    0                1
#  8:       chr1 243709339 244112662      3       1       3        1    0                0
#  9:       chr1 244112662 249250621      3       1       3        1    0                0
# 10:       chr1  71442329  72624878      2       1       3        1    1                1
# 11:       chr1  72624878 102809740      2       1       4        1    1                1

score 2 · Answer 2 · answered Sep 29 '14 at 20:24

Or

transform(df, both = ifelse((Cn_LCIS > 2 & Cn_ILC > 2) | 
                             (Cn_LCIS < 2 & Cn_ILC < 2) |
                              (Cn_LCIS == 2 & Cn_LCIS == 2), 0, 1))

#         Chromosome     Start       End Cn_ILC mCn_ILC Cn_LCIS mCn_LCIS both
# chr1.1        chr1         0  11194349      2       1       2        1    0
# chr1.2        chr1 102809740 104579163      2       1       3        1    1
# chr1.3        chr1 104579163 121311799      2       1       2        1    0
# chr1.4        chr1  11194349  11492125      2       1       3        1    1
# chr1.5        chr1  11492125  71442329      2       1       2        1    0
# chr1.6        chr1 144009053 157140292      1       1       1        1    0
# chr1.7        chr1 157140292 243709339      2       1       1        1    1
# chr1.8        chr1 243709339 244112662      3       1       3        1    0
# chr1.9        chr1 244112662 249250621      3       1       3        1    0
# chr1.10       chr1  71442329  72624878      2       1       3        1    1
# chr1.11       chr1  72624878 102809740      2       1       4        1    1

Gregor Thomas · Answer 3 · 2018-07-17T21:41:51.007

1

The problem with your code is that your innermost ifelse doesn't have an "else" argument. If you just add , 0 inside the innermost ifelse, your code will run. Thad said, some of the other answers are cleaner.

edited Jul 17 '18 at 21:41

answered Sep 29 '14 at 20:24

Gregor Thomas

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score 1 · Answer 4 · answered Sep 29 '14 at 20:55

1

And another possibility is to use with or within

with(df, {
    cb <- cbind(Cn_LCIS, Cn_ILC)
    aa <- (cb > 2) | (cb < 2) | (cb[1] == cb[2])
    (!(aa[,1] == aa[,2]))+0
})
# [1] 0 1 0 1 0 0 1 0 0 1 1

answered Sep 29 '14 at 20:55

Rich Scriven

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score 1 · Answer 5 · answered Sep 29 '14 at 21:23

1

More tersely:

with(df, sign((Cn_LCIS-2)*(Cn_ILC-2))-(Cn_ILC != Cn_LCIS) < 0)*1
# [1] 0 1 0 1 0 0 1 0 0 1 1

answered Sep 29 '14 at 21:23

josliber

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Conditionals in R

5 Answers5