Displaying 20 results from an estimated 3000 matches similar to: "Colour each letter of a text string in a plot"
2012 Oct 21
1
Changing a for loop to a function using sapply
Apparently there is one or more concepts that I do not fully understand
from the descriptions of a function and the apply material. I have
been reading the mail from this forum and have learned much but, in this
case, what I have been reading here and from the manual isn't enough.
The following code produces what I want with the for loop. From what I
have read from this forum, a for
2009 Sep 20
3
statistics
The myoglobin sequence, with reference number NM_005368 in Gen bank, has the
following
frequencies of DNA nucleotides:
A C G T
237 278 309 242
Do these data provide sufficient evidence, at the 1% level of significance,
that the DNA nucleotides
have an unequal distribution, that is the DNA nucleotides are not evenly
utilised?
Clearly state your hypothesis, test statistic and conclusion.
2018 May 03
3
Package for Molecular Properties
All
Is there a package or library that will, given a nucleotide sequence
1. calculate the extinction coefficient at 260 nm for (Beer-Lambert's law)
2. calculate molecular weight
3. return it's complementary sequence
I was able to find several packages that can do similar calculations for an amino acid sequence for proteins but none for nucleic acids.
Any pointers, etc. would be
2018 May 03
0
Package for Molecular Properties
library(sos)
(mp <- findFn('{molecular properties}'))
????? ** found 7 matches in 4 packages and opened two web pages in my
default browser with (a) the 7 matches and (b) the 4 packages. The first
function was something for amino acids, like you suggested.? Two others
returned compound and substance information from PubChem.
????? Does this help?
????? Spencer
On
2010 Jul 19
3
"ACCTGMX" to "1223400" in R?
Hi,
I am a newbie in R and was working on some DNA data represented as strings
of A,C,T and G (also wild-character like M and X). I use the Bioconductor
package in R. Currently I need to convert a string of the form "ACCTGMX" to
"1223400" i.e. A is replaced by 1, C with 2, T with 3, G with 4 and any
other character with a 0. I checked with 'replace' and also with a
2007 Nov 26
1
visualizing nucleotide sequence properties
Hi there,
I am looking for R-packages that can help me visualize properties on
nucleotide sequences. I want to display sequences in the 1-100K base range
as lines and plot features above and below those lines.
Any ideas would be welcome.
Thanks,
Bernd
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2006 Aug 21
1
Escaping " ' " character
Dear all:
I have a character object x with ' (single-quote)
character.
x <- c('"hydrolase activity","actin
binding","3',5'-cyclic-nucleotide phosphodiesterase
activity")
I want to write a function that will identify ' and
replaces with \'
myf <- function(term){
if (grep("'",term))
{
2010 Feb 20
0
new package RFLPtools
The new package RFLPtools is available on CRAN.
RFLPtools provides analysis functions for DNA fragment molecular weights
(e.g.\ derived from RFLP-analysis) and nucleotide sequence similarities.
It aims mainly at the identification of similar or identical fragment
patterns to evaluate the amount of different genotypes gained from
environmental samples during diversity studies and at further
2010 Feb 20
0
new package RFLPtools
The new package RFLPtools is available on CRAN.
RFLPtools provides analysis functions for DNA fragment molecular weights
(e.g.\ derived from RFLP-analysis) and nucleotide sequence similarities.
It aims mainly at the identification of similar or identical fragment
patterns to evaluate the amount of different genotypes gained from
environmental samples during diversity studies and at further
2012 Apr 26
2
Memoize and vectorize a custom function
My goal is simple: calcuate GC content of each sequence in a list of
nucleotide
sequences. I have figured out how to vectorize, but all my attempts at
memoization failed.
Can you show me how to properly memoize my function?
There is a StackOverflow post on the subject of memoization, but it does not
help me:
http://stackoverflow.com/questions/7262485/options-for-caching-memoization-hashing-in-r
2007 Jan 28
2
reposTools
Dear List,
I tested the example in the reposTools vignette:
library(reposTools);
Loading required package: tools
genRepos("Test
Repository", "http://biowww.dfci.harvard.edu/~jgentry/","newRepos");
Error in rep.int(colnames(x), nr) : unimplemented type 'NULL' in 'rep'
Could someone help me out with this one?
I'd appreciate all help....
I am
2004 Dec 29
6
numeric(0)
Dear all,
I am trying to calculate a score for a string sequence consisting of
the following four letters: ACGT.
I have got a matrix giving the scores for each pair of letters.
So for example the string ACCT has got the pairs: AC, CC and CT.
The matrix has got the following form:
names<-c("A","C","G","T");
mscore<-matrix(0,4,4);
2007 Apr 24
0
new version of seqinR
Dear useRs,
The seqinR package is a library of utilities to retrieve and analyse
biological sequences.
A new version of seqinR, seqinR 1.0-7, has been released on CRAN.
Here is a summary of changes:
o A new *experimental* function extractseqs() to download
sequences thru zlib compressed sockets from an ACNUC server is released.
Preliminary tests suggest that working with about 100,000
2007 Apr 24
0
new version of seqinR
Dear useRs,
The seqinR package is a library of utilities to retrieve and analyse
biological sequences.
A new version of seqinR, seqinR 1.0-7, has been released on CRAN.
Here is a summary of changes:
o A new *experimental* function extractseqs() to download
sequences thru zlib compressed sockets from an ACNUC server is released.
Preliminary tests suggest that working with about 100,000
2012 Feb 16
1
help with ancestral.pars in phangorn package
Hello, I'm struggling with understanding the output on the ancestral.pars()
command from the phangorn package, I'm new to doing phylogenetic analyses
using R.
I used it on nucleotide data, and it works fine, I'm just not sure how to
read the output.
The output is phyDat class, and outputs a matrix for each node/leaf in the
tree. I figured out that the matrix columns represent the four
2017 Aug 04
1
legend and values do not match in ggplot
I have following codes for ggplots. The legends are given in the plot do
not match with the values specified in the codes given below. Your helps
highly appreciated.
Greg
library(ggplot2)
p <- ggplot(a,aes(x=NO_BMI_FI_beta ,y=FI_beta ,color= Super.Pathway))+
theme_bw() +theme(panel.border=element_blank()) +
geom_point(size=3)
p2<-p+scale_color_manual(name="Super.Pathway",
2001 Oct 06
0
calculating DNA mismatch distributions for large populations
Hi all,
I am interested in calculating and displaying the distributions of
pairwise comparisons between DNA sequences in populations. The
comparisons are the number of nucleotide sites that differ between the
two sequences (mismatches). My sequences are stored in a vector of
strings. There is an additional vector of the same length that
provides the indices to the DNA sequences. Finally, I
2008 Dec 09
2
motif search
Hi,
I am very new to R and wanted to know if there is a package that, given
very long nucleotide sequences, searches and identifies short (7-10nt)
motifs.. I would like to look for enrichment of certain motifs in
genomic sequences.
I tried using MEME (not an R package, I know), but the online version
only allows sequences up to MAX 60000 nucleotides, and that's too short
for my needs..
2007 Nov 26
1
looking for packages that visualize nucleotide sequence properties
Hi there,
I am looking for R-packages that can help me visualize properties on
nucleotide sequences. I want to display sequences in the 1-100K base range
as lines and plot features above and below those lines.
Any ideas would be welcome.
Thanks,
Bernd
2009 Mar 24
2
Legend containing maths symbol and values of variables
I need to have the maths symbol for >= in the legend, and to
substitute threshold variable with its value. Somehow, various
attempts weren't successful. Please help.
threshold <- 0.5
plot(NA, xlab="", ylab="", main="", axes=F, xlim=c(0,1), ylim=c(0,1),
xaxs="i", yaxs="i")
legend(x=0, y=1, fill=c("orange", "white",