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.4...@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 <dwinsem...@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 <dwinsem...@comcast.net
> > > <mailto:dwinsem...@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]]
> > > >
> > > > ______________________________________________
> > > > R-help@r-project.org <mailto:R-help@r-project.org> mailing list
> > > -- To UNSUBSCRIBE and more, see
> > > >
> https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/r-help__;!!KwNVnqRv!XmQVDL6oNnVVTyIGSfa2u7ps0SpI04MnrWnfq7eXZ0Zz-POPe5r-P4jj2eq-EE8$
> > > > PLEASE do read the posting guide
> > >
> https://urldefense.com/v3/__http://www.R-project.org/posting-guide.html__;!!KwNVnqRv!XmQVDL6oNnVVTyIGSfa2u7ps0SpI04MnrWnfq7eXZ0Zz-POPe5r-P4jj5SGdDSU$
> > > > and provide commented, minimal, self-contained, reproducible
> code.
> > >
> >
> > [[alternative HTML version deleted]]
> >
> > ______________________________________________
> > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> >
> https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/r-help__;!!KwNVnqRv!XmQVDL6oNnVVTyIGSfa2u7ps0SpI04MnrWnfq7eXZ0Zz-POPe5r-P4jj2eq-EE8$
> > PLEASE do read the posting guide
> >
> https://urldefense.com/v3/__http://www.R-project.org/posting-guide.html__;!!KwNVnqRv!XmQVDL6oNnVVTyIGSfa2u7ps0SpI04MnrWnfq7eXZ0Zz-POPe5r-P4jj5SGdDSU$
> > and provide commented, minimal, self-contained, reproducible code.
> >
>
> [[alternative HTML version deleted]]
>
> ______________________________________________
> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
>
> https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/r-help__;!!KwNVnqRv!XmQVDL6oNnVVTyIGSfa2u7ps0SpI04MnrWnfq7eXZ0Zz-POPe5r-P4jj2eq-EE8$
> PLEASE do read the posting guide
> https://urldefense.com/v3/__http://www.R-project.org/posting-guide.html__;!!KwNVnqRv!XmQVDL6oNnVVTyIGSfa2u7ps0SpI04MnrWnfq7eXZ0Zz-POPe5r-P4jj5SGdDSU$
> and provide commented, minimal, self-contained, reproducible code.
>
[[alternative HTML version deleted]]
______________________________________________
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
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.
