grep using a character vector with multiple patterns

Question

I am trying to use grep to test whether a vector of strings are present in an another vector or not, and to output the values that are present (the matching patterns).

I have a data frame like this:

FirstName Letter   
Alex      A1
Alex      A6
Alex      A7
Bob       A1
Chris     A9
Chris     A6

I have a vector of strings patterns to be found in the "Letter" columns, for example: c("A1", "A9", "A6").

I would like to check whether the any of the strings in the pattern vector is present in the "Letter" column. If they are, I would like the output of unique values.

The problem is, I don't know how to use grep with multiple patterns. I tried:

matches <- unique (
    grep("A1| A9 | A6", myfile$Letter, value=TRUE, fixed=TRUE)
)

But it gives me 0 matches which is not true, any suggestions?

Answer 1

In addition to @Marek's comment about not including fixed==TRUE, you also need to not have the spaces in your regular expression. It should be "A1|A9|A6".

You also mention that there are lots of patterns. Assuming that they are in a vector

toMatch <- c("A1", "A9", "A6")

Then you can create your regular expression directly using paste and collapse = "|".

matches <- unique (grep(paste(toMatch,collapse="|"), 
                        myfile$Letter, value=TRUE))

Answer 2

Good answers, however don't forget about filter() from dplyr:

patterns <- c("A1", "A9", "A6")
>your_df
  FirstName Letter
1      Alex     A1
2      Alex     A6
3      Alex     A7
4       Bob     A1
5     Chris     A9
6     Chris     A6

result <- filter(your_df, grepl(paste(patterns, collapse="|"), Letter))

>result
  FirstName Letter
1      Alex     A1
2      Alex     A6
3       Bob     A1
4     Chris     A9
5     Chris     A6

Answer 3

This should work:

grep(pattern = 'A1|A9|A6', x = myfile$Letter)

Or even more simply:

library(data.table)
myfile$Letter %like% 'A1|A9|A6'

Answer 4

Based on Brian Digg's post, here are two helpful functions for filtering lists:

#Returns all items in a list that are not contained in toMatch
#toMatch can be a single item or a list of items
exclude <- function (theList, toMatch){
  return(setdiff(theList,include(theList,toMatch)))
}

#Returns all items in a list that ARE contained in toMatch
#toMatch can be a single item or a list of items
include <- function (theList, toMatch){
  matches <- unique (grep(paste(toMatch,collapse="|"), 
                          theList, value=TRUE))
  return(matches)
}

Answer 5

Have you tried the match() or charmatch() functions?

Example use:

match(c("A1", "A9", "A6"), myfile$Letter)

Answer 6

To add to Brian Diggs answer.

another way using grepl will return a data frame containing all your values.

toMatch <- myfile$Letter

matches <- myfile[grepl(paste(toMatch, collapse="|"), myfile$Letter), ]

matches

Letter Firstname
1     A1      Alex 
2     A6      Alex 
4     A1       Bob 
5     A9     Chris 
6     A6     Chris

Maybe a bit cleaner... maybe?

Answer 7

Not sure whether this answer has already appeared...

For the particular pattern in the question, you can just do it with a single grep() call,

grep("A[169]", myfile$Letter)

Answer 8

Take away the spaces. So do:

matches <- unique(grep("A1|A9|A6", myfile$Letter, value=TRUE, fixed=TRUE))

Answer 9

Using the sapply

 patterns <- c("A1", "A9", "A6")
         df <- data.frame(name=c("A","Ale","Al","lex","x"),Letters=c("A1","A2","A9","A1","A9"))



   name Letters
1    A      A1
2  Ale      A2
3   Al      A9
4  lex      A1
5    x      A9


 df[unlist(sapply(patterns, grep, df$Letters, USE.NAMES = F)), ]
  name Letters
1    A      A1
4  lex      A1
3   Al      A9
5    x      A9

Answer 10

I suggest writing a little script and doing multiple searches with Grep. I've never found a way to search for multiple patterns, and believe me, I've looked!

Like so, your shell file, with an embedded string:

 #!/bin/bash 
 grep *A6* "Alex A1 Alex A6 Alex A7 Bob A1 Chris A9 Chris A6";
 grep *A7* "Alex A1 Alex A6 Alex A7 Bob A1 Chris A9 Chris A6";
 grep *A8* "Alex A1 Alex A6 Alex A7 Bob A1 Chris A9 Chris A6";

Then run by typing myshell.sh.

If you want to be able to pass in the string on the command line, do it like this, with a shell argument--this is bash notation btw:

 #!/bin/bash 
 $stingtomatch = "${1}";
 grep *A6* "${stingtomatch}";
 grep *A7* "${stingtomatch}";
 grep *A8* "${stingtomatch}";

And so forth.

If there are a lot of patterns to match, you can put it in a for loop.