## User: Erik Wright

Erik Wright130
Reputation:
130
Status:
Trusted
Location:
Website:
http://DECIPHER.codes/
digitalwright
Scholar ID:
Last seen:
4 months, 1 week ago
Joined:
1 year, 3 months ago
Email:
d************@gmail.com

#### Posts by Erik Wright

<prev • 16 results • page 1 of 2 • next >
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... It looks like that worked!  Thanks for your help. ...
written 9 months ago by Erik Wright130
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... The latest version of RSQLite (on CRAN) broke my package, DECIPHER, in both the devel and release branches.  I have patched the devel branch so that it should work in the next build, but I do not understand the instructions on how to merge the changes into the release branch.  Does anyone have the m ...
written 9 months ago by Erik Wright130 • updated 9 months ago by Martin Morgan ♦♦ 22k
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... The outputs of DistanceMatrix, including examples, are described in: ?DistanceMatrix Generally, it is a matrix containing the distance between each pair of input sequences.  The distance is 1 - the similarity (fraction of sites that are identical). Homology is not well defined in this context, b ...
written 9 months ago by Erik Wright130
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... Just to clarify, do you mean that you would like to get a distance matrix? d <- DistanceMatrix(bod_aa) And then look at the distances to a specific sequence (e.g., #1)? d[1,] ...
written 9 months ago by Erik Wright130
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... Thanks for clarifying your question.  The sequences are numbered (indexed) according to their order in the imported file.  You can query the sequence headers from the database, for example with: desc <- dbGetQuery(dbConn, 'select description from Seqs where identifier is "Genome2"') desc\$descri ...
written 13 months ago by Erik Wright130
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... Thanks for your interest in DECIPHER. The synteny object that is output by FindSynteny is defined in Synteny-class, see: ?Synteny-class Since you have 3 genomes, your Synteny object will be a 3 x 3 matrix, each each cell containing a list.  Therefore, synteny[[6]] corresponds to the lower tria ...
written 13 months ago by Erik Wright130
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... Of course, simply add a conditional above the AlignSeqs() call: if (length(combAA) > 1) aligned_list[[i]] <- AlignSeqs(combAA) ...
written 13 months ago by Erik Wright130
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... This error means that you are trying to combine disparate classes.  Probably because the variable seq needs to be converted to an AAStringSet: seq <- AAStringSet(seq) ...
written 13 months ago by Erik Wright130
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... The error essentially says that you are trying to index a function.  Probably your sequences are not in a variable called seq.  Since seq() is a base function in R, it thinks you are trying to subset this function rather than an XStringSet.  Note that I inherited the variable named seq from your que ...
written 13 months ago by Erik Wright130
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... Regarding your first bulleted question, you can alter the names of your XStringSet after import: names(allemmAA) <- gsub("(.*?) .*", "\\1", names(allemmAA)) Regarding your second bulleted question, you can make a new XStringSet with the sequences that you want to align, and provide that to Ali ...
written 13 months ago by Erik Wright130

#### Latest awards to Erik Wright

Scholar 15 months ago, created an answer that has been accepted. For A: Is it possible to import a multiple fasta alignemnt (.mfa) file into DECIPHER?
Scholar 15 months ago, created an answer that has been accepted. For A: Colour a phylogenetic tree, based on column in DECIPHER?
Scholar 15 months ago, created an answer that has been accepted. For A: Is it possible to do an alignment to a chosen reference sequence in DECIPHER?

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