Di Cook | R-bloggers

plotting individual values within multiple groups together with their means

July 23, 2024 | Di Cook

In this post I show how groupScatterPlot(), function of the rnatoolbox R package can be used for plotting the individual values in several groups together with their mean (or other statistics). I think this is a useful function for plotting grouped dat...

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Inferring the gender of the subjects from RNAseq BAM files

July 17, 2024 | Di Cook

In this post I show how getGender(), function can be used for inferring the gender of the studied subjects from their binary alignment bam files. The gender can be a source of unwanted variation within the data, for which you may want to ad...

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Assessing the number of mapped reads in several bam files

July 16, 2024 | Di Cook

Recently I have started to organize my commonly used functions related to quality assessment and analyzing RNAseq data into an R package. It is called rnatoolbox and it is available here. In this post I introduce getMappedReadsCount(), i.e. a function ...

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adhan package: retreiving and aligning the prayer times in R

April 1, 2024 | Di Cook

The adhan package is available here ! The prayer times cannot always be estimated accurately in some places such as countries located in higher latitudes (e.g. the Nordic countries) . as for instance during midsummer time the Fajr may b...

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Hierarchical clustering, cutting the tree and colouring the tree leaves based on sample classes

December 19, 2022 | Di Cook

Unsupervised machine learning methods such as hierarchical clustering allow us to discover the trends and patterns of similarity within the data. Here, I demonstrate by using a test data, how to apply the Hierarchical clustering on columns of a test da...

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Fixed vs. random effects for browsing data – a simulation

July 7, 2022 | Di Cook

When you work with trace data — data that emerge when people interact with technology — you will notice that such data often have properties that open up questions about statistical modelling. I currently work with browsing records, obtained a...

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Fixed effects vs. random effects for web browsing data – a simulation

June 23, 2022 | Di Cook

When you work with trace data — data that emerge when people interact with technology — you will notice that such data often have properties that open up questions about statistical modelling. I currently work with browsing records, obtained at s...

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Battery Storage ROI Analysis

December 30, 2021 | Di Cook

It's been a while since my last post and I'm taking my occasional blog in a different direction.Over the years I've learned that utility tariffs, although hard to follow, vary widely. They can have a significant financial impact on behind-the-meter activities, depending on the numbers.The map below shows ... [Read more...]

Bootstrapping the Zero Curve from IRS Swap Rates using R code

July 18, 2021 | Di Cook

This post explains how to generate the zero curve from market swap rates using bootstrapping. For the same 5-Year Libor IRS which is dealt with the previous post, we use Excel illustrations for clear understanding and then make a R code. Boot...

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Correlation in R ( NA friendliness, accepting matrix as input data, returning p values, visualization and Pearson vs Spearman)

May 27, 2021 | Di Cook

Many times, in our projects, we may needed to compare different factors to one another, and study whether they are linearly dependent. These information can also help us to detect covariates and define suitable design formulas for our analysis that wou...

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Maintining the data frame fromat when indexing

April 7, 2021 | Di Cook

Occasionally when indexing data frames the format is converted, leading to confusing consequences. As for instance, when indexing to select a single column the result is a 'numeric' or 'integer' vector. The following demonstrates this :&nbs...

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Measuring effect size in ALDEx2

March 1, 2021 | Di Cook

I'm in the throes of submitting a paper on effect sizes in ALDEx2, and so I thought I would take a stab at a nice concise blog post to summarize and simplify. Effect sizes are standardized mean differences between groups, and are designed to conve...

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Measuring effect size in ALDEx2

March 1, 2021 | Di Cook

I'm in the throes of submitting a paper on effect sizes in ALDEx2, and so I thought I would take a stab at a nice concise blog post to summarize and simplify. Effect sizes are standardized mean differences between groups, and are designed to conve...

[Read more...]

Speeding up aldex.effect()

February 21, 2021 | Di Cook

I've been optimizing various functions in ALDEx2 on Bioconductor to make it more efficient. One bottleneck has been the aldex.effect() function which calculates an effect size for the difference between distributions. I will write a separate... [Read more...]

New Book: "Computational Genomics with R"

February 10, 2021 | Di Cook

It costs now 299$ now to sequence your genome [https://nebula.org/whole-genome-sequencing-dna-test/]. It is getting cheaper to generate genomic data and more of it is coming through. We can't see the same trend for the people who can analyze the ...

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New Book: "Computational Genomics with R"

February 10, 2021 | Di Cook

It costs now 299$ now to sequence your genome [https://nebula.org/whole-genome-sequencing-dna-test/]. It is getting cheaper to generate genomic data and more of it is coming through. We can't see the same trend for the people who can analyze the ...

[Read more...]

R-bloggers

R news and tutorials contributed by hundreds of R bloggers

Articles by Di Cook

plotting individual values within multiple groups together with their means

Inferring the gender of the subjects from RNAseq BAM files

Assessing the number of mapped reads in several bam files

adhan package: retreiving and aligning the prayer times in R

Hierarchical clustering, cutting the tree and colouring the tree leaves based on sample classes

Fixed vs. random effects for browsing data – a simulation

Fixed effects vs. random effects for web browsing data – a simulation

Battery Storage ROI Analysis

Bootstrapping the Zero Curve from IRS Swap Rates using R code

Correlation in R ( NA friendliness, accepting matrix as input data, returning p values, visualization and Pearson vs Spearman)

Maintining the data frame fromat when indexing

Measuring effect size in ALDEx2

Measuring effect size in ALDEx2

Speeding up aldex.effect()

New Book: "Computational Genomics with R"

New Book: "Computational Genomics with R"

Trades Jan. 5, 2021

Trades Jan. 5, 2021

Trades Jan. 4, 2021

Trades Jan. 4, 2021

Articles by Di Cook

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