Your "file1.fas" contains one sequence?
I can't see how that would work to produce a distance matrix.
Please show the output of:
str(Seqs2)
--
You need to understand what a distance matrix is, and what merge() does.
Consider:
x <- data.frame(l1 = c("a", "a", "g"),
l2 =
Thanks for your answer.
First, concerning the function read.dna and dist.gene, they come from the
package ape which is downloaded with pegas.
Here the code that I did for one sequence and which works:
##Code
Seqs1 <- "file1.fas"
Seqs2 <- read.dna(Seqs1, "fasta")
Dist <- dist.gene(Seqs2, method
Myriam -
This is the right list in principle, all the packages you use are CRAN
packages, not Bioconductor.
However I am at a loss as to how you wrote your code: both pegas and seqinr
have "read.()" functions, but neither has read.dna(); similarly both
pegas and seqinr have "dist.()"
"Do not work" does not work (in providing sufficient info). See the Posting
guide linked below for how to post an intelligible question.
HOWEVER, I suspect you would do better posting on te Bioconductor list
where they are much more likely to know what "fasta" files look like and
might even have
Hello!
I need your help. I am trying to calculate the pairwise differences between
sequences from several fasta files.
I would like for each of my DNA alignments (fasta files), calculate the
pairwise differences and then:
- 1. Combine all the data of each file to have one file and one histogram
Hello all,
I am trying to plot a simple choropleth, something I’ve done a while ago using
rworldmap and also (if I recall correctly) ggplot2, but I am failing to draw
the map at all and failing (I think) to merge my data properly with the
shapefile. Thank you for help with a basic question.
Dear Terry,
I added a hex sticker to the effects package, and there will be one in the next
versions of the car and Rcmdr packages. I put a pdf with the hex sticker in
install/docs, and display it with the function effectsHexsticker(); see
?effectsHexsticker. I imagine that there are other
Better posted on r-package-devel list, no?
Cheers,
Bert
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, Jan 21, 2019 at 9:52 AM Therneau, Terry M., Ph.D.
I've created a hex sticker for survival. How should that be added to the
package
directory? It's temporarily in man/figures on the github page.
Terry T.
(Actually, the idea was from Ryan Lennon. I liked it, and we found someone with
actual
graphical skills to execute it. )
> -Original Message-
> From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of Michael
> Friendly
> Check out the `matlib` package on CRAN and devel on github:
Very nice! Thanks for the pointer.
Steve E
***
This
Hi everyone,
I'm new in trying Shiny app in R and for the following question I need your
help. I have a Random Forest model built with Caret Package on iris data set
and then with Shiny I need a UI which I can upload a .csv file as the test set
and give it to the trained model and then see
11 matches
Mail list logo
