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
Thanks
Ana
how to load data frame where numeric will be numeric instead of character
8 messages · Bert Gunter, Ana Marija, David Winsemius +1 more
I count 8 fields in your data and 9 names in your heading ?? 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 1:38 PM Ana Marija <sokovic.anamarija at gmail.com> 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
Thanks
Ana
[[alternative HTML version deleted]]
______________________________________________ R-help at 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.
7th fileld, Direction contains only "+" and "-"
On Mon, Jun 1, 2020 at 3:46 PM Bert Gunter <bgunter.4567 at gmail.com> wrote:
I count 8 fields in your data and 9 names in your heading ?? 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 1:38 PM Ana Marija <sokovic.anamarija at gmail.com> 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
Thanks
Ana
[[alternative HTML version deleted]]
______________________________________________ R-help at 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.
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 at 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.
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 at 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 at 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.
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 at comcast.net
> <mailto:dwinsemius at 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 at r-project.org <mailto:R-help at 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.
>
[[alternative HTML version deleted]]
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 at 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 at comcast.net
<mailto:dwinsemius at 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 at r-project.org <mailto:R-help at 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.
[[alternative HTML version deleted]]
______________________________________________ R-help at 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.
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 at 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 at 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 at comcast.net
<mailto:dwinsemius at 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 at r-project.org <mailto:R-help at r-project.org> mailing list
-- To UNSUBSCRIBE and more, see
>
> PLEASE do read the posting guide
> and provide commented, minimal, self-contained, reproducible
code.
[[alternative HTML version deleted]]
______________________________________________ R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
PLEASE do read the posting guide
and provide commented, minimal, self-contained, reproducible code.
[[alternative HTML version deleted]]
______________________________________________ R-help at 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.