User: Caroline Grisbach Meissner

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Brazil/Curitiba/UFPR
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Posts by Caroline Grisbach Meissner

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Comment: C: GenomicRanges: identify overlapping regions, get intersection between each overl
... This is exactly what I was looking for! Thanks a lot!   ...
written 9 months ago by Caroline Grisbach Meissner0
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Comment: C: GenomicRanges: identify overlapping regions, get intersection between each overl
... I’ve just used the ovlp data frame I posted above (question). You may copy and paste its content to a text editor and save as “hg19.ucsc.final.txt”. My file was a csv, so I used read.csv. Let me know if this is enough  or tell me how could I provide a reproducible example. ...
written 9 months ago by Caroline Grisbach Meissner0
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Comment: A: GenomicRanges: identify overlapping regions, get intersection between each overl
... Unfortunately, I got an error message: ovlp <- read.csv("hg19.ucsc.final.txt",sep=",",header=T) ovlp <- ovlp[,c(1,6,7,3,4)] colnames(ovlp) <- c('chr','start','end','strand','id') ovlp$gene <- ovlp$id ovlp$spos <- ovlp$start ovlp$epos <- ovlp$end ovlp$str <- ovlp$strand gr &l ...
written 9 months ago by Caroline Grisbach Meissner0
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Comment: A: GenomicRanges: identify overlapping regions, get intersection between each overl
... Hi Michael, I would like to save this data into a csv document in order to use as a reference file for further manipulations outside the R environment. But it would be also interesting to have this data as a .RData file. My most wanted final output would be like this: seqnames start end width id ...
written 9 months ago by Caroline Grisbach Meissner0
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Comment: C: GenomicRanges: identify overlapping regions, get intersection between each overl
... > sessionInfo() R version 3.4.2 (2017-09-28) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu precise (12.04.5 LTS) Matrix products: default BLAS: /home/cgrisbach/programme/R-3.4.2/lib64/R/lib/libRblas.so LAPACK: /home/cgrisbach/programme/R-3.4.2/lib64/R/lib/libRlapack.so locale:  [ ...
written 9 months ago by Caroline Grisbach Meissner0
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GenomicRanges: identify overlapping regions, get intersection between each overlapping pair and add gene coordinates (start, end, strand and ids)
... I have a GRange object containing a list of genes. The genomic coordinate might be unique but the gene's id may repeat from a few to several times. I would like to get a file containing all the overlapping genes, their intersection and information (start,end,strand and id) for each matching pair wi ...

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