User: ssabri

gravatar for ssabri
ssabri20
Reputation:
20
Status:
New User
Location:
Last seen:
8 months, 2 weeks ago
Joined:
2 years, 11 months ago
Email:
s*****@g.ucla.edu

Posts by ssabri

<prev • 17 results • page 1 of 2 • next >
3
votes
1
answer
156
views
1
answer
Finding the nearest n genes from a genomic loci
... I am aware of the nearest() function but I believe this is limited to finding the nearest single gene to a loci. Is there a way to compute the n nearest genes for a genomic loci? I ultimately want to do this for a genomicranges object that is segmented into approximately 3 million non-overlapping ra ...
genomicranges written 8 months ago by ssabri20 • updated 8 months ago by Michael Lawrence10k
0
votes
1
answers
323
views
1
answers
Comment: C: Make window around TSS and get values from another data.frame for bins of the sp
... I think the problem is that some transcripts have the same start and end position and these are not preserved as separate entries in subsetByOverlap. This seems to work but is VERY slow:  scores_list <- list() for(r in seq(1,length(exp_granges))){ scores_around_tss <- score(subsetByOverlap ...
written 11 months ago by ssabri20
0
votes
1
answers
323
views
1
answers
Comment: C: Make window around TSS and get values from another data.frame for bins of the sp
... Hi Michael,  I was wondering if you could help me out here. I am creating a new Granges object with the expression data and reducing the range to only the TSS, then I draw a window around the TSS. The exp_granges object looks correct to me. Now I want to subset the scores data.frame with these wind ...
written 11 months ago by ssabri20
2
votes
1
answer
323
views
1
answer
Make window around TSS and get values from another data.frame for bins of the specified window
... I would like to take the "start_position" for each gene in my data.frame and draw a window of 100000 bases upstream and 100000 bases downstream (each in 200 base windows, so 500 windows upstream/downstream of the "start_position") and intersect the window with a granges object that has a score colum ...
chipseq genomicranges granges R written 11 months ago by ssabri20 • updated 11 months ago by Michael Lawrence10k
0
votes
1
answers
303
views
1
answers
Comment: C: Add columns to granges object that sum score around range
... Excellent. I think this is working properly. I have set up my code like so:  rolling_sum <- function(x, window=5) { w <- resize(IRanges(seq_along(x), width=1L), window/unique(width(x)), fix="center") w <- restrict(w, 1L, rep(end(seqnames(x)), width(seqnames(x)))) sum(extractList(x$s ...
written 11 months ago by ssabri20
0
votes
1
answers
303
views
1
answers
Comment: C: Add columns to granges object that sum score around range
... Hi Michael -- I'm thinking more about this and I think it might be best to center on the midpoint of the range for each row and then compute a sum forward and backwards of the midpoint. For example, for a sum of scores within a 10000 window, we look 5000 upstream and 5000 downstream. Does that make ...
written 11 months ago by ssabri20
0
votes
1
answers
303
views
1
answers
Comment: C: Add columns to granges object that sum score around range
... Hi and thank you for your reply. I would like a window to begin at the start of the range and go 10000 upstream. So for the first row the range is 1-200 and I want to compute the sum of scores between 1-10000 and add this number to the metadata columns. The second row range is 201-400 so I want to c ...
written 11 months ago by ssabri20
0
votes
1
answer
303
views
1
answer
Add columns to granges object that sum score around range
... I have a wig file that I've read into a granges-like object using a function that I wrote that calls the `rtracklayer` package: read_wig <- function(x, format='wig', genome='mm9') { suppressMessages(library(rtracklayer)) merged_wig <- import.wig(x, format=format, genome=gen ...
rtracklayer granges R grang written 11 months ago by ssabri20 • updated 11 months ago by Michael Lawrence10k
0
votes
2
answers
584
views
2
answers
Comment: C: Using IRanges to find gene TSS that overlap a window
... It appears this does the same as the above code? How would I restrict the overlap such that the overlap counts only if the TSS is included within the window?  ...
written 16 months ago by ssabri20
0
votes
2
answers
584
views
2
answers
Using IRanges to find gene TSS that overlap a window
... I only want to find genes that have start positions located within a defined range window. If there are no overlaps I want to return NAs for the column fields that describe the overlap. However if there is an overlap with a gene start, then I want to return the gene start and end locations as well a ...
iranges granges R written 16 months ago by ssabri20 • updated 16 months ago by Haibo.Liu0

Latest awards to ssabri

Popular Question 2.9 years ago, created a question with more than 1,000 views. For Deseq2 error estimating size factors -- zeros in count matrix

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 232 users visited in the last hour