Hi Jim,
not in this case, but thanks for asking!
Ana
On Mon, Jun 1, 2020 at 10:04 PM Jim Lemon wrote:
>
> So recombination sticks out its foot before us. Do you want to account
> for gene linkage?
>
> JIm
>
> On Tue, Jun 2, 2020 at 11:55 AM Ana Marija
> wrote:
> >
> > Hi Jim
> >
> > >
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 wrote:
> Agreed!
>
> However, there may still be a problem, as read.table()
So recombination sticks out its foot before us. Do you want to account
for gene linkage?
JIm
On Tue, Jun 2, 2020 at 11:55 AM Ana Marija wrote:
>
> Hi Jim
>
> > neu3<-neu1[!(neu1$Marker %in% Marker3),]
> > dim(neu3)
> [1] 18579
> > nep3<-nep1[!(nep1$Marker %in% Marker3),]
> > dim(nep3)
> [1]
Hi Jim
> neu3<-neu1[!(neu1$Marker %in% Marker3),]
> dim(neu3)
[1] 18579
> nep3<-nep1[!(nep1$Marker %in% Marker3),]
> dim(nep3)
[1] 55629
> ret3<-ret1[!(ret1$Marker %in% Marker3),]
> dim(ret3)
[1] 34939
If I do:
nn1<-merge(neu1,nep1,by=c("Marker","Chr"))
Hi David,
that is a great point!
Yes indeed some are non unique:
> dim(neu1)
[1] 3742845 9
> length(unique(neu1$Marker))
[1] 3741858
> length(unique(nep1$Marker))
[1] 3745560
> dim(nep1)
[1] 3746550 9
> length(unique(ret1$Marker))
[1] 3743494
> dim(ret1)
[1] 3743494 9
How
Hi Ana,
If I add another 6 rows to neu1, 2 to nep1 and one to ret1 and modify
the "Marker" field so that there is one more match, I get the result I
expect. I think that the program logic is correct. I can't say why
ret1 has fewer lines. If there aren't too many mismatches, maybe
checking the
On 6/1/20 5:40 PM, Ana Marija wrote:
Hi Jim,
thank you so much for getting back to me. I tried your code and this is
what I get:
dim(neu2)
[1] 3740988 9
dim(nep2)
[1] 3740988 9
dim(ret2)
[1] 3740001 9
I think I would need to have the same number of lines in all 3 data
Dear Ana and Jim,
On 2020-06-01 19:40 -0500, Ana Marija wrote:
> > dim(neu2)
> [1] 3740988 9
> > dim(nep2)
> [1] 3740988 9
> > dim(ret2)
> [1] 3740001 9
Jim's code works out of the box directly from
the email ... I get:
[1] 6 9
[1] 4 9
[1] 4 9
On 2020-06-01 19:40 -0500, Ana
Hi Jim,
thank you so much for getting back to me. I tried your code and this is
what I get:
> dim(neu2)
[1] 3740988 9
> dim(nep2)
[1] 3740988 9
> dim(ret2)
[1] 3740001 9
I think I would need to have the same number of lines in all 3 data frames.
Can you please advise.
Cheers
Hi Ana,
Not too hard, but your example has all the "marker" fields in common.
So using a sample that will show the expected result:
neu1<-read.table(text="Chr BP Marker MAF A1 A2 Direction pValue N
1 10012 1:10012:G:T 0.229925 T G + 0.650403 1594
1 10827 1:10827:C:T
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,
Good morning Bruce & Abby,
The fruit bats of Sydney have retreated to their camps so I can
finally answer your last two queries. Attached is a plot of your data
set on a 100 x 100 grid. This is how I did it:
bfs<-read.csv("Procen_sample.csv")
dim(bfs)
names(bfs)
library(plotrix)
# set the matrix
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"
Hello,
I have 3 data frames which have about 3.4 mill lines (but they don't have
exactly the same number of lines)...they look like this:
> neu1=neu[order(neu$Marker),]
> head(neu1)
ChrBP Marker MAF A1 A2 Direction pValueN
209565 1 10012 1:10012:G:T
absolutely restore .rt as a valid transcript file name.
.st goes back to at least S-Plus and if my memory serves, to S.
.rt was constructed by analogy.
the .rout and .sout are excessively verbose, rather recent additions.
Additions, not replacements.
Rich
On Mon, Jun 1, 2020 at 4:47 PM Alex
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
On 6/1/20 1:37 PM, Ana Marija wrote:
Hello,
I have a dataframe like this:
ChrBP Marker MAF A1 A2 Direction pValueN
1 10 10625 10:10625:A:G 0.416562 G A - 0.558228 1594
2 10 10645 10:10645:A:C 0.215182 C A - 0.880622 1594
On 6/1/20 4:46 PM, Alex Branham via ESS-help wrote:
On Mon 01 Jun 2020 at 14:23, William McCoy via ESS-help
wrote:
(setq auto-mode-alist (append '(("\\.[Rr]t\\'" . R-transcript-mode))
auto-mode-alist))
That line no longer has any effect on ESS and my .Rt suffix no longer
works;
7th fileld, Direction contains only "+" and "-"
On Mon, Jun 1, 2020 at 3:46 PM Bert Gunter 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."
> --
On Mon 01 Jun 2020 at 14:23, William McCoy via ESS-help
wrote:
> (setq auto-mode-alist (append '(("\\.[Rr]t\\'" . R-transcript-mode))
> auto-mode-alist))
>
> That line no longer has any effect on ESS and my .Rt suffix no longer
> works; ESS expects .Rout as the suffix.
>
> How can I
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
wrote:
>
Hello,
I have a dataframe like this:
ChrBP Marker MAF A1 A2 Direction pValueN
1 10 10625 10:10625:A:G 0.416562 G A - 0.558228 1594
2 10 10645 10:10645:A:C 0.215182 C A - 0.880622 1594
...
which I load with:
NEU <-
Please move this discussion to R-package-devel.
On June 1, 2020 12:43:01 PM PDT, Adelchi Azzalini
wrote:
>
>
>> On 1 Jun 2020, at 21:35, Sorkin, John
>wrote:
>>
>> Regardless of whether the people who wrote the Matlab code you used
>as a reference, or who wrote the paper that published the
> On 1 Jun 2020, at 21:35, Sorkin, John wrote:
>
> Regardless of whether the people who wrote the Matlab code you used as a
> reference, or who wrote the paper that published the idea that you included
> in your package are cited as co-authors of your package, the coders and
> authors
Regardless of whether the people who wrote the Matlab code you used as a
reference, or who wrote the paper that published the idea that you included in
your package are cited as co-authors of your package, the coders and authors
should be identified as the people from whom you borrowed the idea
> On 1 Jun 2020, at 19:37, Michael Dewey wrote:
>
> You might get better answers on the list dedicated to package development
> r-pkg-devel
This is a good suggestion. Thanks, Michael.
Some initial search of that list did not lead to any indication,
but I will have a second look.
Best
Hi,
I'm probably biased.
But my package, bivariate, contains a wrapper for KernSmooth::bkde2D,
which can produce both 3D surface plots and (pretty) contour plots of
bivariate kernel density estimates, conveniently.
https://cran.r-project.org/web/packages/bivariate/vignettes/bivariate.pdf
(pages
Dear R users, with some delay I would like to make you aware of the recent
CRAN release of *collapse* (https://CRAN.R-project.org/package=collapse), a
large new C/C++ based package for advanced and high-performance general
purpose data transformation in R.
*collapse* has 2 main objectives:
1. To
I have been using ESS mainly for R for over 20 years. I use R less
frequently in recent years and I have not tried to use transcript mode
for a while. I have always used .Rt as the suffix for my R transcript
files. I have hundreds of them and I have retained the following line
in my
You might get better answers on the list dedicated to package
development r-pkg-devel
This may have already been discussed there so a quick look at the
archive might also help you.
On 01/06/2020 17:34, Adelchi Azzalini wrote:
The new version of a package which I maintain will include a new
The new version of a package which I maintain will include a new function which
I have ported to R from Matlab.
The documentation of this R function indicates the authors of the original
Matlab code, reference to their paper, URL of the source code.
Question: is this adequate, or should I
El sáb., 30 de may. de 2020 6:31 p. m., Carlos Ortega <
c...@qualityexcellence.es> escribió:
> Hola,
>
> He podido subir y bajar un fichero .RData a una cuenta de GooglDrive.
> A la hora de subirlo, he tenido primeramente que autorizar que desde R
> pudiera interaccionar con esa cuenta de
You can read it in as 'raw'
input <- file('your.xlsx', open = 'rb') # open as binary
excel_file <- readBin(input, raw(), 1e8) # make sure you read in all the file
close(input)
output <- file('your_new.xlsx', 'wb')
writeBin(excel_file, output)
close(output)
===
You might check that n %% 1 == 0.
(Factorials do exist for fractional numbers -- check e.g. factorial(6.5). And
please don't send HTML because, well, you can see the result below)
- pd
> On 1 Jun 2020, at 12:49 , Vahid Borji wrote:
>
> I am writing a code for the factorial function. My code
I am writing a code for the factorial function. My code is as follows:
> f<- function(n){+ factorial <- 1+ if( n < 0 )+ print("Factorial of negative
> numbers is not possible")+ else if( n == 0 )+ print("Factorial of 0 is 1")+
> else {+ for(i in 1:n)+ factorial <- factorial * i+
35 matches
Mail list logo
