[R] looping through rows of a logical matrix for combination with and testing of a numeric vector
bgunter.4567 at gmail.com
Thu Dec 3 16:58:00 CET 2015
I should have added -- is this homework? There is a no homework policy
on this list.
"Data is not information. Information is not knowledge. And knowledge
is certainly not wisdom."
-- Clifford Stoll
On Thu, Dec 3, 2015 at 7:54 AM, Bert Gunter <bgunter.4567 at gmail.com> wrote:
> Have you spent any time with an R tutorial or two? I ask, because you
> do not seem to have much knowledge of the language and its features.
> Have you made any effort to figure this out yourself? -- if so, show
> us your code and where/how it goes wrong. I ask, because you seem to
> be asking this list to do your work for you, which is not its purpose.
> Bert Gunter
> "Data is not information. Information is not knowledge. And knowledge
> is certainly not wisdom."
> -- Clifford Stoll
> On Thu, Dec 3, 2015 at 7:28 AM, debra ragland via R-help
> <r-help at r-project.org> 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 "standard" vector, such that the return is a matrix of logical values indicating TRUE if there is a match to the standard and FALSE where there is no match.
>> An example;
>> mylist=c("AAEBCC", "AABDCC", "AABBCD")
>> list.2 <- strsplit(mylist, split=NULL)
>> # setting a standard for comparison
>> std.string <- "AABBCC"
>> standard <- unlist(strsplit(std.string, split=NULL))
>> #create a logical matrix
>> mat<-sapply(list.2, function(x) x==standard)
>> [,1] [,2] [,3]
>> [1,] TRUE TRUE TRUE
>> [2,] TRUE TRUE TRUE
>> [3,] FALSE TRUE TRUE
>> [4,] TRUE FALSE TRUE
>> [5,] TRUE TRUE TRUE
>> [6,] TRUE TRUE FALSE
>> Where the number of columns is the same length as the original input strings I compared (15) and the number of rows corresponds is the same as the number of strings from the input (99).
>> I also have a named numeric vector(of length 15)--where the "names" of the the values match those of the columns of the logical matrix. For the example
>> x2 = runif(3, 5.0, 7.5)
>> names(x2) = 1:3
>> 1 2 3
>> 5.352611 7.058169 6.993105
>> For each row in the in the logical matrix I want to combine the logical values with the values from the numeric vector so that I can run a wilcox.test using those values that are "TRUE" against those that are "FALSE".
>> For instance if each row&vector pairing was a mini data.frame it would look like
>> df=data.frame(x2, mat[3,])
>> 1 5.352611 FALSE
>> 2 7.058169 TRUE
>> 3 6.993105 TRUE
>> wilcox.test(df) #based on all true values vs. all false values
>> How can this be achieved?
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>> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
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