User: ssabri

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ssabri10
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Posts by ssabri

<prev • 16 results • page 1 of 2 • next >
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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 10 days ago by ssabri10
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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 10 days ago by ssabri10
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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 11 days ago by ssabri10 • updated 10 days ago by Michael Lawrence9.9k
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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 18 days ago by ssabri10
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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 18 days ago by ssabri10
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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 18 days ago by ssabri10
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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 18 days ago by ssabri10 • updated 18 days ago by Michael Lawrence9.9k
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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 5 months ago by ssabri10
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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 5 months ago by ssabri10 • updated 5 months ago by Haibo.Liu0
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Building a pseudo-network based on correlations
... I have clustered a few points and have computed the mean of each cluster as a landmark point for that cluster. I have then computed a correlation matrix among all landmark points to see which are most similar. Now I'd like to *connect* each landmark points to its two most similar neighbors. Since th ...
R ggplot2 written 15 months ago by ssabri10 • updated 15 months ago by Matthias Z.20

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Popular Question 2.0 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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