User: andreucat91

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Posts by andreucat91

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Comment: C: diffHic: minimum counts per bin
... Thank you. Does it make sense to find bin1 vs bin1 (in the diagonal), differentialy expressed? ...
written 2.5 years ago by andreucat910
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Comment: C: diffHic: minimum counts per bin
... Thank you. I wanted to ask another question. I know that the lower the resolution, the best. In very low resolutions, we can have a very sparse matrix and we would filter too much bins. Let's say I have matrices for 20.000, 40.000, 100.000bp. Do you know how to choose the best resolution for differe ...
written 2.5 years ago by andreucat910
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Comment: C: ggbio: integrate different plots
... Thank you for your reply. To draw genes, what I use is the following: p2 <- autoplot(txdb, which=genes_subset, label.color = "black", color = "brown", fill = "brown") + theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank()) it draws gene structures including exons, int ...
written 2.5 years ago by andreucat910
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Comment: C: diffHic: minimum counts per bin
... Thank you for your reply. I've modified my post. ...
written 2.5 years ago by andreucat910
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ggbio: integrate different plots
... I am wondering if something like this (A and B):     is possible with `ggbio`. ...
ggbio written 2.5 years ago by andreucat910 • updated 2.5 years ago by Michael Lawrence11k
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diffHic: minimum counts per bin
... Hi, I've loaded my matrix this way: bin.coords <- import("./1000000.bed") bin.coords <- as(bin.coords, "GRanges") raw <- read.table("./1000000.txt") gi <- GInteractions(raw$V1, raw$V2, bin.coords, mode="reverse") iset1 <- InteractionSet(as.matrix(raw$V3), gi) iset1$totals <- col ...
edger diffhic written 2.5 years ago by andreucat910
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regioneR: error when verbose=TRUE
... Using the last version available (1.4.2), calling overlapPermTest with verbose=TRUE, it throws the following error: Error in random.evaluate[, i] : incorrect number of dimensions I think there's somthing around line 157 of permTest.R, since this error happens at line 174 when verbose=TRUE. When v ...
regioner written 2.9 years ago by andreucat910 • updated 2.9 years ago by bgel30
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Error while smoothing BS-seq data with bsseq
... I have a problem when I try to smooth my data with the package bsseq. This data comes from bismark and has been previously loaded to R with read.bismark function without problems. You have the commands I used below: library("bsseq") files_chh = list.files(path = ".", pattern = "CHH") meth <- re ...
bsseq written 3.7 years ago by andreucat910 • updated 2.1 years ago by Nikolay.Oskolkov0

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