replace asterisks in dataframe with NA's - r

Question

Here's my dataframe df
I'm trying:
df=data.frame(rbind(c(1,"*","*"),c("*",3,"*"))
df2=as.data.frame(sapply(df,sub,pattern="*",replacement="NA"))
It doesn't work because of the asterisk but I'm getting mad trying to replace it.

Answer 1

If you just have * in (meaning its not like ab*de) your data.frame, then, you can do ths without regex:
df[df == "*"] <- NA

Answer 2

Both solutions here address an object already in your workplace. If possible (or at least in the future) you can make use of the na.strings argument in read.table. Notice that it is plural "strings", so you should be able to specify more than one character to treat as NA values.
Here's an example: This just writes a file named "readmein.txt" to your current working directory and verifies that it is there.
cat("V1 V2 V3 V4 V5 V6 V7\n
2 * * * * * 2\n
1 2 * * * * 1\n", file = "readmein.txt")
list.files(pattern = "readme")
# [1] "readmein.txt"
Here's read.table with the na.strings argument in action.
read.table("readmein.txt", na.strings="*", header = TRUE)
# V1 V2 V3 V4 V5 V6 V7
# 1 2 NA NA NA NA NA 2
# 2 1 2 NA NA NA NA 1
Update: Objects already in your workplace
I see another problem with the other two answers: They both result in character (or rather factor) variables, even when the column should have possibly been numeric.
Here's an example. First, we create an example dataset. For fun, I've added another character to be treated as NA: ".".
temp <- data.frame(
V1 = c(1:3),
V2 = c(1, "*", 3),
V3 = c("a", "*", "c"),
V4 = c(".", "*", "3"))
temp
# V1 V2 V3 V4
# 1 1 1 a .
# 2 2 * * *
# 3 3 3 c 3
str(temp)
# 'data.frame': 3 obs. of 4 variables:
# $ V1: int 1 2 3
# $ V2: Factor w/ 3 levels "*","1","3": 2 1 3
# $ V3: Factor w/ 3 levels "*","a","c": 2 1 3
# $ V4: Factor w/ 3 levels ".","*","3": 1 2 3
Let's make a copy, and then solve this in what I would consider the most obvious "R" way:
temp1 <- temp
temp1[temp1 == "*"|temp1 == "."] <- NA
Looks OK...
temp1
# V1 V2 V3 V4
# 1 1 1 a <NA>
# 2 2 <NA> <NA> <NA>
# 3 3 3 c 3
... but I presume that V2 and V4 should have been numeric....
str(temp1)
# 'data.frame': 3 obs. of 4 variables:
# $ V1: int 1 2 3
# $ V2: Factor w/ 3 levels "*","1","3": 2 NA 3
# $ V3: Factor w/ 3 levels "*","a","c": 2 NA 3
# $ V4: Factor w/ 3 levels ".","*","3": 1 NA 3
Here's a workaround:
temp2 <- read.table(text = capture.output(temp), na.strings = c("*", "."))
temp2
# V1 V2 V3 V4
# 1 1 1 a NA
# 2 2 NA <NA> NA
# 3 3 3 c 3
str(temp2)
# 'data.frame': 3 obs. of 4 variables:
# $ V1: int 1 2 3
# $ V2: int 1 NA 3
# $ V3: Factor w/ 2 levels "a","c": 1 NA 2
# $ V4: int NA NA 3
Update 2: (Yet another) alternative
It might be more appropriate to make use of type.convert which is described as a "helper function for read.table" on its help page. I haven't timed it, but my guess is that it would be faster than the workaround I mentioned above, with all the benefits.
data.frame(
lapply(temp, function(x) type.convert(
as.character(x), na.strings = c("*", "."))))

Answer 3

You should put up a full reproducible example, people will be more inclined to help when you make it easy for em. Anywho...
dat <- data.frame(a=c(1,2,'*',3,4), b=c('*',2,3,4,'*'))
> dat
a b
1 1 *
2 2 2
3 * 3
4 3 4
5 4 *
> as.data.frame(sapply(dat,sub,pattern='\\*',replacement=NA))
a b
1 1 <NA>
2 2 2
3 <NA> 3
4 3 4
5 4 <NA>

Answer 4

This could work (It's a pretty flexible) but there's other great solutions already. Arun's solution is my typical approach but created replacer for new R (little experience with the command line) users. I wouldn't recommend replacer for anyone with even a bit of experience.
library(qdap)
replacer(dat, "*", NA)