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

[Ana Marija]

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?

Thanks
Ana

On Mon, Jun 1, 2020 at 4:13 PM David Winsemius <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
> >
> >       [[alternative HTML version deleted]]
> >
> > ______________________________________________
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>

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