[R] how to load data frame where numeric will be numeric instead of character

[David Winsemius]

On 6/1/20 2:17 PM, Ana Marija wrote:
> HI David,
>
> this is the problem:
>
> > NEP <- read.table("gokind.nephropathy.fin", 
> header=T,stringsAsFactors=FALSE)
> > sapply(NEP,class)
>         Chr          BP      Marker         MAF          A1        A2
> "character" "character" "character" "character" "character" "character"
>   Direction      pValue           N
>
> So even entries like Chr, BP, MAF....are characters while they should 
> be numeric
> > head(NEP)
>   Chr        BP           Marker      MAF A1 A2 Direction pValue    N
> 1  10 100000625 10:100000625:A:G   0.4156  G  A         + 0.484813 1641
> 2  10 100000645 10:100000645:A:C 0.216027  C  A         +  0.73597 1641
>
>
> Can you please tell me what colClasses=colClassvec suppose to do?


I could tell you, but I think instead that you should read the 
documentation for the `read.table` function.


-- 

David

>
> Thanks
> Ana
>
> On Mon, Jun 1, 2020 at 4:13 PM David Winsemius <dwinsemius using comcast.net 
> <mailto:dwinsemius using comcast.net>> wrote:
>
>
>     On 6/1/20 1:37 PM, Ana Marija wrote:
>     > Hello,
>     >
>     > I have a dataframe like this:
>     >
>     >    Chr        BP           Marker      MAF A1 A2 Direction 
>      pValue    N
>     > 1  10 100000625 10:100000625:A:G 0.416562  G  A         -
>     0.558228 1594
>     > 2  10 100000645 10:100000645:A:C 0.215182  C  A         -
>     0.880622 1594
>     > ...
>     >
>     > which I load with:
>     > NEU <- read.table("gokind.neuropathy.fin",
>     header=T,stringsAsFactors=FALSE)
>     >
>     > and every column is numeric. How to say have all numeric ones
>     stay numeric
>     > like: Chr, BP, MAF, pValue, N
>
>
>     I cannot figure out what the problem is. You say every column is
>     numeric. It's not possible to have a column that contains the value
>     "10:100000625:A:G" be numeric.
>
>
>     If you meant to say the every column was character, then the answer
>     might be:
>
>
>     colClassvec <- rep("numeric",9)
>     colClassvec[ c(3,5:7)] <- "character"
>
>     NEU <- read.table("gokind.neuropathy.fin",
>     header=T,stringsAsFactors=FALSE, colClasses=colClassvec)
>
>     -- 
>     David.
>
>     >
>     > Thanks
>     > Ana
>     >
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>     >
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