User: sinha.puja

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sinha.puja10
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Posts by sinha.puja

<prev • 19 results • page 1 of 2 • next >
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Comment: C: Suggestion for circlize package in R for plotting the datasets
... The code is below: circos.initializeWithIdeogram(species = "rn6") circos.par("track.height"=0.20) circos.genomicTrackPlotRegion(data = yc,ylim = NULL, numeric.column = 4, + panel.fun = function(region,value,...) { + ...
written 5 weeks ago by sinha.puja10
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Comment: C: Suggestion for circlize package in R for plotting the datasets
... It's very dense and I don't see the individual dots except two separate bands in the track based on my two range of data sets. ...
written 6 weeks ago by sinha.puja10
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Comment: C: Suggestion for circlize package in R for plotting the datasets
... Thank you for the tutorial but still I did not get the appropriate answer. ...
written 6 weeks ago by sinha.puja10
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Suggestion for circlize package in R for plotting the datasets
... Hi All, I have large data set with methylation values ranging from 0-1. The data contains around 3 million rows of values corresponding to the chromosomal locations. I want to split/sort my data for plot using circos plot. I thought of doing like sorting the value range 0.2-0.4 as hypomethylation c ...
circlize written 6 weeks ago by sinha.puja10
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Comment: C: Plotting DMRs (Differentially Methylated Regions) using Gviz package in R
... Thanks for your suggestion, I will save my data in .csv format. Reply for quick questions as follows: 1. When I did `head (data1)`, it looks fine to me. 2. I don't know how to connect that part, may be that was missing while plotting. 3. Yes, when I try to load Gviz and BS genome, it was asking for ...
written 7 weeks ago by sinha.puja10 • updated 7 weeks ago by RamRS26k
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Plotting DMRs (Differentially Methylated Regions) using Gviz package in R
... Hi All, I have a file list consisting of Chromosome, Start , End & Methylation Difference in the following format in excel: Chrom Start End Meth. Diff chr1 38565900 38566000 -0.20276818 chr1 38870400 38870500 -0.342342342 chr1 39469400 39469500 ...
R gviz written 7 weeks ago by sinha.puja10 • updated 7 weeks ago by RamRS26k
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Comment: A: Error while running readTranscriptFeatures in methylkit
... gene.obj = readTranscriptFeatures("P:/New folder/YOUNGCONTROL.bed") After using the above command second time I got the following error: Calculating intron coordinates... **Error in .Call2("solve_user_SEW0", start, end, width, PACKAGE = "IRanges") : In range 1: at least ...
written 12 weeks ago by sinha.puja10 • updated 12 weeks ago by genomax80k
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Comment: C: Error while running readTranscriptFeatures in methylkit
... After using the above command I got an error mentioned below: Error: cannot allocate vector of size 157.0 Mb In addition: Warning message: In eval(quote(list(...)), env) : NAs introduced by coercion Anyone please help. ...
written 3 months ago by sinha.puja10
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Error while running readTranscriptFeatures in methylkit
... I am using methylkit package for annotation of methylated CpG sites into exons/introns/exon-intron boundary etc. For that I have my .bed file with list of CpGs with methylation values and I downloaded refGene file from the ucsc browser. I am using the following step1 code for getting the results: ...
R written 3 months ago by sinha.puja10
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Problem in installing methyl kit in R 3.6.1
... Hi, I was trying to install methyl kit package in R 3.6.1 with the following command but it has error showing that BiocManager::install("methylkit" , dependencies = TRUE) library(methylkit) **Error in library(methylkit) : there is no package called ‘methyl ...
R written 3 months ago by sinha.puja10 • updated 3 months ago by ATpoint31k

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