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Plotting differentially methylated bases on an ideogram

June 21, 2012
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(This article was first published on Recipes, scripts and genomics, and kindly contributed to R-bloggers) To leave a comment for the author, please follow the link and comment on their blog: Recipes, scripts and genomics. R-bloggers.com offers daily e-mail updates about R news and tutorials on topics such as: Data science, Big Data, R jobs, visualization (ggplot2, Boxplots, maps,...

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Plotting differentially methylated bases on an ideogram

June 21, 2012
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Plotting differentially methylated bases on an ideogram

Ideogram is a popular way to show genomic features in relation to chromosome sizes and chromosomal location in bulk. Recently, we have shown differentially methylated CpGs on a chromosomal ideogram in our PLoS Genetics paper. Although it doesn't always make sense to show differentially methylated bases on an ideogram, I'm describing a function below that does a similar...

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DNA methylation (RRBS or target capture) analysis with R

February 20, 2012
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Reduced Representation Bisulfite sequencing (RRBS) is a popular technique for measuring methylation levels across genome. Although it does not have the full genome coverage, it covers many important regions for methylation. Below, I shared a tutorial a...

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DNA methylation (RRBS or target capture) analysis with R

February 20, 2012
By

Reduced Representation Bisulfite sequencing (RRBS) is a popular technique for measuring methylation levels across genome. Although it does not have the full genome coverage, it covers many important regions for methylation. Below, I shared a tutorial a...

Read more »

methylKit: R package for DNA methylation analysis

December 21, 2011
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High-throughput bisulfite sequencing based methods are popular for measuring genome-wide DNA methylation levels. Here is an R package that helps with the analysis of such DNA methylation data. Although, it is still under heavy development current funct...

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methylKit: R package for DNA methylation analysis

December 21, 2011
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High-throughput bisulfite sequencing based methods are popular for measuring genome-wide DNA methylation levels. Here is an R package that helps with the analysis of such DNA methylation data. Although, it is still under heavy development current functionality allows users to do many of the essential data analysis tasks. The package is primarily designed for Reduced...

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knitr: nice alternative for Sweave

December 17, 2011
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I recently discovered knitr for dynamic report generation in R. It seems like a very powerful alternative to Sweave. Particularly, I am interested in png graphic device support (it supports more than 20 graphic devices) and R code formatting.Check it o...

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knitr: nice alternative for Sweave

December 17, 2011
By

I recently discovered knitr for dynamic report generation in R. It seems like a very powerful alternative to Sweave. Particularly, I am interested in png graphic device support (it supports more than 20 graphic devices) and R code formatting.Check it o...

Read more »

Fast(ish) extraction of exon locations from a BED12 file using data.table

March 20, 2011
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Here is a fast R function to extract exon locations from a BED12 file. Note that fast is a relative term, the function below is fast enough for me, may not be fast enough for others :) Anyway, a BED12 file typically has locations of genomic features (t...

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Applying functions on groups: sqldf, plyr, doBy, aggregate or data.table ?

March 17, 2011
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Applying functions on groups: sqldf, plyr, doBy, aggregate or data.table ?

Which one of the sqldf, plyr, doBy and aggregate functions/packages would be faster for applying functions on groups of rows? I was wondering about this earlier in this post.  It seems sqldf would be the fastest according to a post in manipulatr m...

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