Ana Marija
2020-Jun-01 21:17 UTC
[R] how to load data frame where numeric will be numeric instead of character
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. >[[alternative HTML version deleted]]
David Winsemius
2020-Jun-01 22:19 UTC
[R] how to load data frame where numeric will be numeric instead of character
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]]
Bert Gunter
2020-Jun-01 23:35 UTC
[R] how to load data frame where numeric will be numeric instead of character
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. >[[alternative HTML version deleted]]