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

[David Carlson]

It might be easier to diagnose if you can show us what the first ten lines
in your original file look like.

readLines("gokind.nephropathy.fin", n=10)

David L Carlson


On Mon, Jun 1, 2020 at 6:36 PM Bert Gunter <bgunter.4567 using gmail.com> wrote:

> Agreed!
>
> However, there may still be a problem, as read.table() ordinarily would
> read numeric columns correctly (via type.convert()) without the colClasses
> specification.
> So I would suspect that her "numeric" columns contain some non-numeric
> detritus (perhaps "," or some NA symbol). But of course, who knows? -- and
> she should follow David's advice to read the docs anyway.
>
>
> Bert Gunter
>
> "The trouble with having an open mind is that people keep coming along and
> sticking things into it."
> -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )
>
>
> On Mon, Jun 1, 2020 at 3:19 PM David Winsemius <dwinsemius using comcast.net>
> wrote:
>
> >
> > 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
> > >     >
> > >     >       [[alternative HTML version deleted]]
> > >     >
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