Blog Archives

Calling BEDtools from R

February 22, 2011
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BEDtools suite provides command-line functionality when dealing with genomic coordinate based operations, such as overlapping bed files or getting coverage of a bed file over a genome (similar, not exactly same, functionality in R is provided by IRange...

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Access all UCSC wiggle tracks from R and your terminal

February 21, 2011
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rtracklayer package allows you to access most of the UCSC wiggle tracks from R. However, there is another way which might more practical in situations where you need to summarize the wig track scores over a given set of genomic coordinates. Although yo...

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Access all UCSC wiggle tracks from R and your terminal

February 21, 2011
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rtracklayer package allows you to access most of the UCSC wiggle tracks from R. However, there is another way which might more practical in situations where you need to summarize the wig track scores over a given set of genomic coordinates. Although yo...

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Utilizing multiple cores in R

February 8, 2011
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There are a couple of options in R, if you want to utilize multiple cores on your machine. These days my favorite is doMC package, which depends on foreach and multicore packages.in the section below squareroot for each number is calculated in parallel...

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Utilizing multiple cores in R

February 8, 2011
By

There are a couple of options in R, if you want to utilize multiple cores on your machine. These days my favorite is doMC package, which depends on foreach and multicore packages.in the section below squareroot for each number is calculated in parallel...

Read more »

command line options in R: "optparse" package

February 8, 2011
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C/python style option parsing now available in R with "optparse" package. Check the documentation here and see below to see how it [email protected] scripts $ Rscript filter.transcripts.by.ncRNA.R -husage:  usage: filter.transcripts.by.ncRNA.R [op...

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command line options in R: "optparse" package

February 8, 2011
By

C/python style option parsing now available in R with "optparse" package. Check the documentation here and see below to see how it [email protected] scripts $ Rscript filter.transcripts.by.ncRNA.R -husage:  usage: filter.transcripts.by.ncRNA.R [op...

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sqldf and grouping rows in R

February 8, 2011
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In R, you can treat tables (or data.frames as they are called in R) as SQL tables. That means you can query them as you would query a database with SQL commands. This is particularly useful 1) if you know SQL, hahah:)  2) if you have large tabl...

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sqldf and grouping rows in R

February 8, 2011
By

In R, you can treat tables (or data.frames as they are called in R) as SQL tables. That means you can query them as you would query a database with SQL commands. This is particularly useful 1) if you know SQL, hahah:)  2) if you have large tabl...

Read more »

Principal Component Analysis: Which variables contribute most to principal components ?

November 23, 2010
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Principal component analysis (PCA) is a mathematical transformation of possibly(correlated) variables into a number of uncorrelated variables called principal components. The resulting components from this transformation is defined in such a way that t...

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