## User: ssabri

ssabri20
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20
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1 year, 3 months ago
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3 years, 6 months ago
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s*****@g.ucla.edu

#### Posts by ssabri

<prev • 17 results • page 1 of 2 • next >
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... 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 ...
written 16 months ago by ssabri20 • updated 16 months ago by Michael Lawrence11k
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... 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 18 months ago by ssabri20
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... 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 18 months ago by ssabri20
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... 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 ...
written 18 months ago by ssabri20 • updated 18 months ago by Michael Lawrence11k
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... 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 18 months ago by ssabri20
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... 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 18 months ago by ssabri20
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... 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 18 months ago by ssabri20
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... 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 ...
written 18 months ago by ssabri20 • updated 18 months ago by Michael Lawrence11k
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... 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 23 months ago by ssabri20
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... 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 ...
written 23 months ago by ssabri20 • updated 23 months ago by Haibo.Liu0

#### Latest awards to ssabri

Popular Question 3.5 years ago, created a question with more than 1,000 views. For Deseq2 error estimating size factors -- zeros in count matrix

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