User: jhanks1981

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jhanks19810
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Posts by jhanks1981

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Comment: C: Subset GRanges object into new object
... That did it! tscripts_gr <- stack(tscripts, "gene_id") tscripts_gr[tscripts_gr@seqnames == "chr1"] GRanges object with 17531 ranges and 3 metadata columns: seqnames ranges strand | gene_id tx_id tx_name <Rle> & ...
written 24 days ago by jhanks19810
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Comment: A: Subset GRanges object into new object
... I am trying to compare two GTF files. First, I want to subset it so that I'm only including Chr1-22+X+Y from each GTF file. Second, I want to see what features are not common to both objects Third, I want to take each feature and compare the start and end locations between each file. Finally, I ...
written 24 days ago by jhanks19810
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Subset GRanges object into new object
... I have already read a few pages such as this one https://support.bioconductor.org/p/50138/   library(GenomicRanges) library(GenomicFeatures) #make the list of chromosomes to filter by #make the database and transcripts txdb <- makeTxDbFromGFF("Me/inputs/gencode.v19.chr_patch_hapl_scaff.annota ...
genomicranges R subsetting written 24 days ago by jhanks19810

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