User: d r

gravatar for d r
d r150
Reputation:
150
Status:
Trusted
Location:
Israel
Last seen:
1 day ago
Joined:
4 years, 7 months ago
Email:
d*********@gmail.com

Posts by d r

<prev • 30 results • page 1 of 3 • next >
0
votes
1
answer
68
views
1
answer
Drawing a HeatMapList while retaining the original row order of each heat map
... The ComplexHeatmap documenation, under 'Making a list of Heatmaps' states that: "Under default mode, dendrograms from the second heatmap will be removed and row orders will be same as the first one." Is it possible to draw multiple heatmaps from a HeatMapList side by side while retaining the origi ...
complexheatmap written 21 days ago by d r150 • updated 21 days ago by Steve Lianoglou12k
1
vote
1
answer
61
views
1
answer
Problem with using GDC_queryMaf()
... Hello I am trying to use the TCGAbiolinks package to extract mutation data for several types of tumors I am interested in. I am using GDCquery_Maf, using exactly the syntax indicated in the help file: acc.maf <- GDCquery_Maf("ACC") However I then get the error: Error in missing(tumor) : 'm ...
maf tcgabiolinks mutations written 4 weeks ago by d r150 • updated 2 days ago by tiagochst60
0
votes
2
answers
297
views
2
answers
Comment: C: Intersecting a Granges and a GRangesList using within
... Thanks! just what I needed.   ...
written 18 months ago by d r150
0
votes
2
answers
297
views
2
answers
Comment: C: Intersecting a Granges and a GRangesList using within
... @Valerie Obenchain. Thanks for your reply. The output in your example seems what I want. However, In your call to lapply(), you iterate on an object called lst? Can you please tell me what it this object. I did not see it defined in your reply. Thanks again. ...
written 18 months ago by d r150
0
votes
0
answers
226
views
0
answers
Comment: C: ignore.strand option in range() when using GRangesList
... Thanks. I really appreciate the effort! ...
written 18 months ago by d r150
2
votes
2
answers
297
views
2
answers
Intersecting a Granges and a GRangesList using within
... Hello, I have a GRanges (gr) object and a GRangesList (grlist). I want to find elements in grlist that fully overlap elements of gr. That is, I want to know, for a given i and j if there is k such that grlist[j][[k]] is fully contained within gr[i]. It is important that the values of both i and ...
granges grangeslist findoverlaps written 18 months ago by d r150 • updated 18 months ago by Hervé Pagès ♦♦ 12k
1
vote
0
answers
226
views
0
answers
ignore.strand option in range() when using GRangesList
... Hello I note that while the range() function for GRanges objects has an ignore.strand argument, the equivalent function for GRangesList does not have this argument. Is there a particular reason that this option was not included in the GRangesList function? Also, what can I do if I do want to use ...
granges written 18 months ago by d r150
0
votes
2
answers
363
views
2
answers
Comment: C: Intersecting a Granges and a GRangesList elementwise
... Thanks! I did not know that mapply() works on GRangesList. Good to know. ...
written 18 months ago by d r150
0
votes
2
answers
363
views
2
answers
Comment: C: Intersecting a Granges and a GRangesList elementwise
... @Michael Lawerece Thanks for your reply. However,I think neither of your suggestions does what I want. What I want is to know, for a given i if there is k such that grlist[[i]][k] is within gr[i]. For example: gr<-GRanges(seqnames=c('chr1','chr2'), ranges=IRanges(start=c(10,20),end=(50,100)) gr1& ...
written 18 months ago by d r150
2
votes
2
answers
363
views
2
answers
Intersecting a Granges and a GRangesList elementwise
... Hello I have a Granges object (gr) and a GRangesList (grlist) of the same length. I want to intersect them element-wise, that is, I want to know if any element in grlist[[i]] is (fully) contained in gr[i]. I can of course do something of the loop variant: intersect<-lapply(seq(length(gr)), fun ...
genomicranges findoverlaps written 19 months ago by d r150 • updated 18 months ago by Hervé Pagès ♦♦ 12k

Latest awards to d r

Popular Question 17 months ago, created a question with more than 1,000 views. For GRanges DitancetoNearest query

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 320 users visited in the last hour