User: francesca casalino

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Posts by francesca casalino

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Comment: C: GenomicRanges based on indices or more conditions, and add column from match
... Hi, Thank you Michael for your reply.  My problem is trying to add information from df1_all and df2_all only from the intersecting IDs (with the condition that both ranges overlap):      OBJ = data.frame(df1_all[unique(subjectHits(intersect(hits1, hits2))),]) But then how to get the columns in df ...
written 8 weeks ago by francesca casalino50
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GenomicRanges based on indices or more conditions, and add column from match
... I am trying to extract columns based on two conditions from the indices of two overlaps. This is an example:       df1 = data.frame(chr=c("chr1", "chr1"), start=c(20,21), stop=c(28,29), value1=c(1,2))     df2 = data.frame(chr=c("chr1", "chr1", "chr1"), start=c(20,22, 28), stop=c(22,24,34), value2 ...
iranges genomicranges findoverlaps written 8 weeks ago by francesca casalino50
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Answer: A: ChIPseeker question: provide custom csAnno to plots
... Ok sure, thank you for your reply.  ...
written 3.1 years ago by francesca casalino50
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ChIPseeker question: provide custom csAnno to plots
... Hi, I would like to use plotAnnoBar with different categories of classes compared to the default of "Promoter", "5' UTR", "3' UTR",  "Exon", "Intron", "Downstream (<=3kb)", "Intergenic", so I was wondering whether it is possible to go from a data frame of frequencies ("anno.df" in ChIPseeker), t ...
chipseeker written 3.1 years ago by francesca casalino50
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Answer: A: GenomicRanges mapply to all combinations of GRangesList objects
... Thanks very much for your help!  SORRY I realise I gave a bad example because the columns would not be all the same in the data frames! Here is a new example:       gr1 <- GRanges(seqnames = c("chr1", "chr2"), ranges = IRanges(c(7,13), width = 3), strand = c("+", "-"))     gr2 <- GRanges(se ...
written 3.1 years ago by francesca casalino50
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Comment: C: GenomicRanges mapply to all combinations of GRangesList objects
... Great, thank you. Now just trying to figure out how I can get a rbind data frame for the object B, I think I will just resort to looping.  ...
written 3.1 years ago by francesca casalino50
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Comment: C: GenomicRanges mapply to all combinations of GRangesList objects
... Thank you. It is very slow but it may have done something wrong in my original function since the output is not quite what I was looking for with lists of a containing data frames of b, anyway I will try to fix that. Thanks! ...
written 3.1 years ago by francesca casalino50
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GenomicRanges mapply to all combinations of GRangesList objects
... I have two GRange Lists and I am trying to apply countOverlaps function to each combination of the lists and return a list of results like this:     gr1 <-  GRanges(seqnames = "chr2", ranges = IRanges(3, 6),strand = "+", score = 5L, GC = 0.45)     gr2 <- GRanges(seqnames = c("chr1", "chr1"), ...
genomicranges grangeslist mapply written 3.1 years ago by francesca casalino50
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Answer: A: Question about ChiPseeker: plot other values in plotAvgProf2
... Ok thanks, is there a restriction on the values that can be mapped then? I was using the V5 to give an example with the same data you used but I have normalised expression values in V5 that I wanted to map and I was trying with those as well, they range from -20 to +20, but I also wanted to map seve ...
written 3.2 years ago by francesca casalino50
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Answer: A: Question about ChiPseeker: plot other values in plotAvgProf2
... It gives me an error if I try it with "files" as in the Vignette... I must be doing something wrong...   plotAvgProf2(files, weightCol="V5", TxDb=txdb, upstream=3000, downstream=3000) >> preparing promoter regions...     2015-10-13 19:22:57  >> preparing tag matrix...         2015-10 ...
written 3.2 years ago by francesca casalino50

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