User: ssabri

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ssabri20
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Posts by ssabri

<prev • 17 results • page 1 of 2 • next >
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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 7 months ago by ssabri20 • updated 7 months ago by Michael Lawrence10k
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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 9 months ago by ssabri20
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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 9 months ago by ssabri20
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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 9 months ago by ssabri20 • updated 9 months ago by Michael Lawrence10k
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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 9 months ago by ssabri20
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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 9 months ago by ssabri20
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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 9 months ago by ssabri20
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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 9 months ago by ssabri20 • updated 9 months ago by Michael Lawrence10k
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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 14 months ago by ssabri20
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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 14 months ago by ssabri20 • updated 14 months ago by Haibo.Liu0

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