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User: Erik Wright

gravatar for Erik Wright
Erik Wright130
Reputation:
130
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Website:
http://DECIPHER.codes/
Twitter:
digitalwright
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Google Scholar Page
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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Comment: C: Updating release branch from devel
... It looks like that worked!  Thanks for your help. ...
written 9 months ago by Erik Wright130
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Updating release branch from devel
... 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 ...
git written 9 months ago by Erik Wright130 • updated 9 months ago by Martin Morgan ♦♦ 22k
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Comment: C: How to get sequence homology percent from a multiple sequence alignment in DECIP
... 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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Comment: C: How to get sequence homology percent from a multiple sequence alignment in DECIP
... 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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Comment: C: Transform index to chromosome in DECIPHER package
... 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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Answer: A: Transform index to chromosome in DECIPHER package
... 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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Comment: C: Is it possible to do an alignment to a chosen reference sequence in DECIPHER?
... 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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Comment: C: Is it possible to do an alignment to a chosen reference sequence in DECIPHER?
... 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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Comment: C: Is it possible to do an alignment to a chosen reference sequence in DECIPHER?
... 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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Answer: A: Is it possible to do an alignment to a chosen reference sequence in DECIPHER?
... 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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