User: sophialovechan

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3 years, 1 month ago
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Posts by sophialovechan

<prev • 73 results • page 1 of 8 • next >
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Comment: C: Convert Granges list of peaks into consensus counts
... Yes. It does work after I corrected this. But the new problem is that I didn't get any metadata. >myGRangesList GRangesList object of length 3 ...... #myGRangesList shows that there are three different datasets. >consensusToCount <- GenomicRanges::reduce(unlist(myGRangesLis ...
written 11 weeks ago by sophialovechan40
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Comment: C: Convert Granges list of peaks into consensus counts
... I found out the problem with your code. After you run `do.call(c, your.GRangesList)`, you convert GRangesList into a list again. That's why I run into an error. To make your code work, you will have to `GenomicRanges::reduce(GRangesList(do.call(c, your.GRangesList)))`. ...
written 11 weeks ago by sophialovechan40
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Comment: C: Convert Granges list of peaks into consensus counts
... The initial input is a large list and I named it as 'myPeaks'. I used GRangesList(myPeaks) to change the list into a "CompressedGRangesList", as shown below. myGRangesList<-GRangesList(myPeaks) GenomicRanges::reduce(do.call(c, myGRangesList)) class(myGRangesList) [1] "CompressedG ...
written 12 weeks ago by sophialovechan40
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Comment: C: Convert Granges list of peaks into consensus counts
... Should I use the GRangesList here? I got an error. Error in (function (classes, fdef, mtable) : unable to find an inherited method for function 'reduce' for signature '"list"' ...
written 12 weeks ago by sophialovechan40
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Comment: C: Convert Granges list of peaks into consensus counts
... Ok. Thank you very much. ...
written 12 weeks ago by sophialovechan40
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Comment: C: Convert Granges list of peaks into consensus counts
... I didn't understand your code. Do you mind explaining it ? GenomicRanges::reduce(do.call(c, your.GRangesList)) What does c mean? and What am I doing here? Also for bedrolls, what do k1,1 -k2,2n mean? Thank you. I had 'soGGi:::runConsensusRegions' function worked before. But when I used the same ...
written 12 weeks ago by sophialovechan40
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Comment: C: Convert Granges list of peaks into consensus counts
... Hello, I run into the same issue as yours. Did you solve it? ...
written 12 weeks ago by sophialovechan40
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Comment: C: How to do scaling in ComplexHeatmap
... Problem solved. Thanks. ...
written 6 months ago by sophialovechan40
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Comment: C: How to do scaling in ComplexHeatmap
... > Heatmap(data, name="log(CPM)", km=5, col=colorRamp2(c(min(data, na.rm=T), mean(data, na.rm=T), max(data, na.rm=T),c("blue", "white", "red")), bottom_annotation = ha, bottom_annotation_height = unit(4, "mm"), show_row_names = FALSE, show_column_names = FALSE)) Error in colorRamp2(c( ...
written 6 months ago by sophialovechan40 • updated 6 months ago by RamRS24k
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Comment: C: How to do scaling in ComplexHeatmap
... Thank you very much! ...
written 6 months ago by sophialovechan40

Latest awards to sophialovechan

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