User: Robert

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Robert10
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Posts by Robert

<prev • 8 results • page 1 of 1 • next >
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Unintended grey dot in Gviz plots
... When plotting a ```Gviz``` ```DataTrack``` I noticed a grey dot appearing in the center of the plot. ``` library(Gviz) set.seed(13) df <- data.frame(chr = rep("chrI", 30), start = 1:30, end = 1:30, score = rnorm(n = 30, mean = 10, sd = 2)) data.track <- DataTrack(makeGRangesFromDataFrame(df ...
gviz written 25 days ago by Robert10 • updated 15 days ago by Robert Ivanek620
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How to center data points on coordinates (bases) in Gviz?
... I plot my NGS data using the ```Gviz``` library. When I use a ```.bedGraph``` file to construct a ```DataTrack``` the data points appear between genomic coordinates (bases). The same is true for a corresponding ```.bw``` file (not shown in code below). When I first read the ```.bedGraph``` file and ...
gviz written 26 days ago by Robert10
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How to modify centromere depiction in Gviz IdeogramTrack?
... I visualize my NGS data using the ```Gviz``` library. I can create and plot a ```IdeogramTrack``` with the following code. ``` library(Gviz) cyto.bands <- data.frame(chrom = rep("chrI", 4), chromStart = c(0, 148071, 151524, 154977), chromEnd = c ...
gviz written 26 days ago by Robert10
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Answer: A: Extract metadata from GRanges object for every genomic coordinate
... Based on Michael's answer I can achieve my goal with this code: library(GenomicRanges) gr1 <- GRanges( seqnames = Rle("chr1", 3), ranges = IRanges(start = c(1, 2, 8) + 1, end = c(2, 5, 9)), score = 1:3) gr1 # GRanges object with 3 ranges and 1 metadata ...
written 26 days ago by Robert10
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Comment: C: Extract metadata from GRanges object for every genomic coordinate
... Thanks, Michael. The `GPos` containers seem very interesting. However, it seems like with `GPos()` my metadata columns are lost. Do you know a workaround? ...
written 6 weeks ago by Robert10
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Comment: C: Extract metadata from GRanges object for every genomic coordinate
... Thanks, Michael. That's very helpful to fill the uncovered regions. However, I'm still not sure how to get a `GRanges` object with all ranges having width 1. I would like to achieve this, as I have to plot and correlate several scores from different files at the single-nucleotide level. ...
written 6 weeks ago by Robert10
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Comment: C: Extract metadata from GRanges object for every genomic coordinate
... Thanks, Martin. I'm working with `.bedGraph` files (zero-based half-open). That's were the overlapping range for position 2 came from. ...
written 6 weeks ago by Robert10
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Extract metadata from GRanges object for every genomic coordinate
... It is easy enough to extract genomic ranges and associated meta data from a `GRanges` object. ``` library(GenomicRanges) gr1 <- GRanges( seqnames = Rle("chr1", 3), ranges = IRanges(c(1, 2, 8), end = c(2, 5, 9)), score = 1:3) show(gr1) ## GRanges object with 3 ranges and 1 metadata column ...
genomicranges granges written 6 weeks ago by Robert10

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