R help - Feb 2009 - how to separate char and num within a variable

Hi all,

I read in a column which looks like "chr1:000889594-000889638", and
need to break them into three columns like "chr1:",
"000889594" and "000889638". How shall I do in R. Thanks a
lot for your suggestions!

Bill

Bill Hyman wrote:
> Hi all,
>
> I read in a column which looks like "chr1:000889594-000889638",
and need to break them into three columns like "chr1:",
"000889594" and "000889638". How shall I do in R. Thanks a
lot for your suggestions!
>
>   
if strings is your vector of strings, this should do (assuming the
format is stable across all entries):

strsplit(strings, split=':|-')

vQ

on 02/05/2009 05:20 PM Bill Hyman wrote:
> Hi all,
> 
> I read in a column which looks like "chr1:000889594-000889638",
and
> need to break them into three columns like "chr1:",
"000889594" and
> "000889638". How shall I do in R. Thanks a lot for your
suggestions!
See ?strsplit

Vec <- "chr1:000889594-000889638"
> Vec
[1] "chr1:000889594-000889638"

# Use a regular expression, defining the 'split' character
# as either ":" or "-", where the vertical bar means
'or':
> strsplit(Vec, split = ":|-")
[[1]]
[1] "chr1"      "000889594" "000889638"


Note that the split characters are not retained in the result.

Let's presume that you have a column in a data frame of the original
data and wish to split it into 3 columns:

DF <- data.frame(Col = rep(Vec, 10))
> DF
                        Col
1  chr1:000889594-000889638
2  chr1:000889594-000889638
3  chr1:000889594-000889638
4  chr1:000889594-000889638
5  chr1:000889594-000889638
6  chr1:000889594-000889638
7  chr1:000889594-000889638
8  chr1:000889594-000889638
9  chr1:000889594-000889638
10 chr1:000889594-000889638

Note that by default, 'Col' will be a factor and strsplit() expects a
character vector, thus we do the coercion and use do.call() to create a
character matrix, via rbind(), from the result:
> do.call(rbind, strsplit(as.character(DF$Col), split = ":|-"))
      [,1]   [,2]        [,3]
 [1,] "chr1" "000889594" "000889638"
 [2,] "chr1" "000889594" "000889638"
 [3,] "chr1" "000889594" "000889638"
 [4,] "chr1" "000889594" "000889638"
 [5,] "chr1" "000889594" "000889638"
 [6,] "chr1" "000889594" "000889638"
 [7,] "chr1" "000889594" "000889638"
 [8,] "chr1" "000889594" "000889638"
 [9,] "chr1" "000889594" "000889638"
[10,] "chr1" "000889594" "000889638"


See ?regex, ?do.call and ?rbind for more information.

HTH,

Marc Schwartz

Thank you!



----- Original Message ----
From: "markleeds at verizon.net" <markleeds at verizon.net>
To: Bill Hyman <billhyman1 at yahoo.com>
Sent: Thursday, February 5, 2009 3:35:54 PM
Subject: RE: [R] how to separate char and num within a variable

hi: you can do below but there should possibly be a better way so I'm
sending offline in
order to encourage better replies from the guRus. good luck.


temp <- "chr1:000889594-000889638"
temp2 <- strsplit(temp, ":|-")
print(temp2)





"chr1:000889594-000889638",




On Thu, Feb 5, 2009 at  6:20 PM, Bill Hyman wrote:
> Hi all,
> 
> I read in a column which looks like "chr1:000889594-000889638",
and need to break them into three columns like "chr1:",
"000889594" and "000889638". How shall I do in R. Thanks a
lot for your suggestions!
> 
> Bill
> 
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.