R help - Jun 2008 - Creating a Hash from Data.Frame

Hi,

I have the following data frame:
> print(mydatframe)
__DATAFRAME__

   V1    V2 V3
1 1007_s_at  DDR1  discoidin domain receptor tyrosine kinase 1
2 1053_at  RFC2  replication factor C (activator 1) 2, 40kDa
3 117_at  HSPA6  heat shock 70kDa protein 6 (HSP70B')

__END__

Is there a way to create a hash with
V2 as Key and V3 as its value?

- Gundala Viswanath
Jakarta - Indonesia

here is a way:
> x <- read.table(textConnection("#GDS_ID GENE_NAME GENE_DESCRIPTION
GENE_FUNCTION
+ 1007_s_at | DDR1 | discoidin domain receptor tyrosine kinase 1 |
protein-coding
+ 1053_at | RFC2 | replication factor C (activator 1) 2, 40kDa | protein-coding
+ 117_at | HSPA6 | heat shock 70kDa protein 6 (HSP70B') |
protein-coding"), sep="|",
+ strip.white=TRUE, quote='')   # you need strip.white on the
call
> closeAllConnections()
> str(x)
'data.frame':   3 obs. of  4 variables:
 $ V1: Factor w/ 3 levels "1007_s_at","1053_at",..: 1 2 3
 $ V2: Factor w/ 3 levels "DDR1","HSPA6",..: 1 3 2
 $ V3: Factor w/ 3 levels "discoidin domain receptor tyrosine kinase
1",..: 1 3 2
 $ V4: Factor w/ 1 level "protein-coding": 1 1
1
> x
         V1    V2                                          V3             V4
1 1007_s_at  DDR1 discoidin domain receptor tyrosine kinase 1 protein-coding
2   1053_at  RFC2 replication factor C (activator 1) 2, 40kDa protein-coding
3    117_at HSPA6        heat shock 70kDa protein 6 (HSP70B')
protein-coding
> mydata <- character()
> mydata[as.character(x$V2)] <- as.character(x$V3)
> mydata["RFC2"]  #access the data
                                         RFC2
"replication factor C (activator 1) 2, 40kDa"
>
remember to add the 'strip.white=TRUE' on read.table

On Sun, Jun 15, 2008 at 9:53 PM, Gundala Viswanath <gundalav at gmail.com>
wrote:
> Hi,
>
> I have the following data frame:
>
>> print(mydatframe)
>
> __DATAFRAME__
>
>   V1    V2 V3
> 1 1007_s_at  DDR1  discoidin domain receptor tyrosine kinase 1
> 2 1053_at  RFC2  replication factor C (activator 1) 2, 40kDa
> 3 117_at  HSPA6  heat shock 70kDa protein 6 (HSP70B')
>
> __END__
>
> Is there a way to create a hash with
> V2 as Key and V3 as its value?
>
> - Gundala Viswanath
> Jakarta - Indonesia
>
> ______________________________________________
> 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.
>


-- 
Jim Holtman
Cincinnati, OH
+1 513 646 9390

What is the problem you are trying to solve?

"Gundala Viswanath" <gundalav at gmail.com> writes:
> Hi,
>
> I have the following data frame:
>
>> print(mydatframe)
>
> __DATAFRAME__
>
>    V1    V2 V3
> 1 1007_s_at  DDR1  discoidin domain receptor tyrosine kinase 1
> 2 1053_at  RFC2  replication factor C (activator 1) 2, 40kDa
> 3 117_at  HSPA6  heat shock 70kDa protein 6 (HSP70B')
>
> __END__
>
> Is there a way to create a hash with
> V2 as Key and V3 as its value?
This looks like microarray data for which the Bioconductor project
(http://bioconductor.org/biocLite.R) might be useful
> source('http://bioconductor.org/biocLite.R')
> biocLite() # installs a number of pacakges
> biocLite('hgu95av2.db') # a particular chip 'annotation'
file
> library(hgu95av2.db)
> hgu95av2GENENAME[["1053_at"]]
[1] "replication factor C (activator 1) 2,
40kDa"
> hgu95av2SYMBOL[["1053_at"]]
[1] "RFC2"

probe id's are keys, with different 'hash'es underneath and
non-trivial functionality neatly encapsulated.
> openVignette()
and then choose AnnotationDbi for additional examples (or via the Bioc
web site, following the 'Packages' quick link). Also see the archives
and bioc mailing list, mentioned on the site.

Martin
> - Gundala Viswanath
> Jakarta - Indonesia
>
> ______________________________________________
> 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.
-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M2 B169
Phone: (206) 667-2793