RRBS Data analysis with Methylkit

I am having trouble understanding the meaning of the plot given to me by the following code

getMethylationStats(myobj[[1]],plot=TRUE,both.strands=FALSE)

methylation rrbs methylkit r

• 656 views • link

written 2.9 years ago by 296cd367 0

0 answers

No answers yet.

More posts like this

WGBS Data Analysis
written 4.7 years ago by shrinka.genetics 4

Hi I am using the MethylKit package for DMC analysis. My files look like >BC1417Chr21<-read.table ("BC1417-Chr21.txt") > head(BC1417Chr21) Chr base Strand coverage freqC freqT 1 …
Clustering 10X scRNA data based on selected markers
written 5.4 years ago by A 0

Hi I am trying to cluster my single cell data using known markers with the aim of finding cell populations based on expression of specific …
"MethylKit" package for WGBS data
written 6.0 years ago by shrinka.genetics 4

I am using MethyKit package for WBGS data analysis. There it has a step like > meth <- unite(myobj, destrand=FALSE) uniting... Where it unites, if …
Generation of Dendogram on WGBS data
written 6.0 years ago by shrinka.genetics 4

Hi I am working on WGBS data and using MethylKit package. Methykit has its own function to make a dendogram on CpG methylation, but I …
visualizing mutational data using Maftools for reference genome hg19
written 6.0 years ago by nazaninhoseinkhan 53

Dear all, I am trying to do somatic variation analysis using TCGABiolinks package in R 3.6. I want to use hg19 version of human genome. …
True Positive rate of simulation
written 6.1 years ago by Ruolin Liu 0

In your landmark VG [Nat. Biotech paper][1], I am having a little bit of difficulty understanding ROC curve result of [Figure 2A][2]. As far as …
"MethylKit" package for WGBS data
written 6.1 years ago by shrinka.genetics 4

Hello I am working on WGBS data using MethylKIT package. I am trying to analyse few samples whose dimension are not same (see below). What …
scale in R pheatmap
written 7.0 years ago by acfasantos 0

Hi, I am having trouble understanding the scale() function in R. Anyone could explain it to me? Because my clusters change with scale option.
Methylkit using hadoop for DNA analysis
written 11.7 years ago by shalini.ravishankar 1

Hi, Can someone tell me is there a way to do [Methylkit][1] R Package on Hadoop? Please give me some idea on how to proceed …
Class_Code In Isoform-Fpkm-Tracking
written 14.1 years ago by GPR 40

<p>Hello, In the isoform-fpkm-tracking file produced by CuffDiff, I am having trouble, understanding the meaning of class codes, viz, </p> <p><code>class_code =, class_code j, class_code …