User: Malcolm Cook

gravatar for Malcolm Cook
Malcolm Cook1.4k
Reputation:
1,440
Status:
Trusted
Location:
United States
Last seen:
2 days, 3 hours ago
Joined:
12 years, 6 months ago
Email:
m***********@gmail.com

Posts by Malcolm Cook

<prev • 154 results • page 1 of 16 • next >
0
votes
0
answers
56
views
0
answers
coercion to Granges from empty data.frame ==> unexpected behavior ??
... Hello, I find it odd that coersion to GRanges with as fails in the case of an empty data.frame: This works fine: > as(data.frame(SeqID=c('s'),start=c(1),end=c(2)),'GRanges') GRanges object with 1 range and 0 metadata columns: seqnames ranges strand <Rle> <IRanges> ...
granges coercion written 9 days ago by Malcolm Cook1.4k
0
votes
2
answers
104
views
2
answers
Answer: A: get vertex xy coords from igraph mst plot
... The graph does not holds its own plotting coordinates.   Look at ?layout_  ?plot.igraph ?igraph.plotting and you will learn how to get multiple different coordinates sets for the same plot depending upon choice of layout algorithm. To give you a sense: in the following example, the same graph, g, ...
written 4 months ago by Malcolm Cook1.4k
0
votes
2
answers
531
views
2
answers
Comment: C: Extract isoform-specific ranges
... Thanks. I reported your experience as an issue here: checkbox to accept response as answer does not appear in Safari browser #439 ...
written 5 months ago by Malcolm Cook1.4k
0
votes
2
answers
531
views
2
answers
Comment: C: Extract isoform-specific ranges
... To the left of every response to your question you should have the opportunity to click on a "thumb" to give the response +1 points and I think also a check-mark in a circle, which will turn green, which indicates that you have "accepted" the response as an answer.  I could not find documentation on ...
written 5 months ago by Malcolm Cook1.4k
0
votes
2
answers
531
views
2
answers
Comment: C: Extract isoform-specific ranges
... @hwu12 - Glad to help!  The best thanks would be to accept my answer! ...
written 6 months ago by Malcolm Cook1.4k
0
votes
2
answers
531
views
2
answers
Comment: C: Extract isoform-specific ranges
... Yes, except that it does not provide the info present in the revmap, being the association of each range with the to which it is unique isoform which I am assuming (perhaps incorrectly?) is desired result   > subset(GRanges(coverage(u)), score==1L) GRanges object with 2 ranges and 1 metadata c ...
written 6 months ago by Malcolm Cook1.4k
0
votes
2
answers
531
views
2
answers
Answer: A: Extract isoform-specific ranges
... Hello - I expect GenomicRanges:disjoin is your friend for this operation. Look: # editted for tightness and clarity, and to add a final split > g<-GRangesList(GeneA.1 = GRanges(seqnames="x", ranges=IRanges(1, 10), strand="+") + ,GeneA.2 = GRanges(seqnames="x", ranges=IRanges( ...
written 6 months ago by Malcolm Cook1.4k
0
votes
0
answers
213
views
0
answers
HowTo: install just html help on top of existing packages
... Is there an efficient way to install html help ONLY for all existing packages in an R installation some of which are BioConductor packages? ...
bioclite update package installation written 11 months ago by Malcolm Cook1.4k
0
votes
1
answers
1.6k
views
1
answers
Comment: C: Which package to run blast
... I have improved the example to: provide the -remote option (to get job to run at NCBI on their database) omit data.table example (which was extraneous and incorrect) demonstrate use of -entrez_query option, which hints at the power of filtering results using entrez queries. ...
written 18 months ago by Malcolm Cook1.4k
0
votes
1
answers
1.6k
views
1
answers
Answer: A: Which package to run blast
... I recommend not using an R package.  Rather, make system calls to execute blast jobs remotely at NCBI, and get tabular results back in an R data.frame Here is an example: seqs <- ## The sequences to be blasted and their fasta 'deflines' as an character vector. c('>s1','CTTTGTCTTCCCCTA ...
written 18 months ago by Malcolm Cook1.4k

Latest awards to Malcolm Cook

Popular Question 2.8 years ago, created a question with more than 1,000 views. For Is Bioconductor 3.0 compatible with R 3.1.2?
Scholar 2.8 years ago, created an answer that has been accepted. For A: Importing a .txt file with multiple headers into R
Centurion 12.5 years ago, created 100 posts.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 169 users visited in the last hour