Hello,
I have tried this 2 ways and I keep coming to a dead end as I am not very
proficient in R.
I have a logical matrix, where I would like to generate every row-wise pair of
logical values for further testing. That is row1, row2; row 1, row3 etc.
Ideally, I would like to assign a pre-genera
Sorry for the repost, but I want to clarify that I am trying to apply the
wilcox.test to every pairwise combination of rows i.e. row 1 with row 2, row 1
with row 3, row 1 with row 4 and so on until all row combinations have been
achieved.
I've made some corrections.
On Wednesday, December 9,
Hello All,
I have written the following loop which will apply/split the same vector of
numbers (pc1.eigv) to each (logical) row of a matrix and run a wilcox.test on
those values that line up with TRUE and those that line up with FALSE. It works
fine. However, I am now interested in using the sa
st
B.
On Dec 3, 2015, at 10:28 AM, debra ragland via R-help
wrote:
> I have read in a sequence alignment and have done the necessary steps to
> separate and store the elements of the original input into a new list of
> character vectors. I have compared the sequence list to a &q
of the matrix:
x <- mat[3, x2]
y <- mat[3, !x2]
Or: use the formula version of wilcox.test as explained in ?wilcox.test
B.
On Dec 3, 2015, at 10:28 AM, debra ragland via R-help
wrote:
> I have read in a sequence alignment and have done the necessary steps to
> separate a
I have read in a sequence alignment and have done the necessary steps to
separate and store the elements of the original input into a new list of
character vectors. I have compared the sequence list to a "standard" vector,
such that the return is a matrix of logical values indicating TRUE if the
I think I am making this problem harder than it has to be and so I keep getting
stuck on what might be a trivial problem.
I have used the seqinr package to load a protein sequence alignment containing
15 protein sequences;
> library(seqinr) > x =
read.alignment("proteins.fasta",format="f
The
> function prcomp() returns a list in which the matrix x contains the rotated
> values of your input. Assuming that your "variable names" are the rownames of
> your input, you can plot them with text().
>
> Something like (untested):
>
> myPCA <-
Hello,
A colleague of mine prepared a PCA plot of my data and I have no clue how he
did it. My original data set contains 15 variables and 64 observations. I have
been trying to figure out how he did it on my own, and I have asked but he's
swamped so his response is taking longer than usual. A
I have 15 protein sequences of 99 amino acids each. After doing some looking
around I have found that there are several ways you can read sequences into R
and do pairwise or multiple alignments. I, however, do not know how to probe
changes at specific positions. For instance, I would like to kno
Please help,I am spinning my wheels behind what should be a pretty simple
solution. I found a solution by asking another question on here but it seems to
not be effective on all my files of similar make up to the test case. I am
simply trying to read data into R, group/order it by chain and atom
Hello,
I am trying to fit my data to the default autoregressive models in R. I'm
trying to apply the effectiveSize function from the coda package to a list of
data frames using;
sapply(splits, function(x) coda::effectiveSize(x["V5"]))
However when I do, I get the error;
Error in ar.yw.defa
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