Publications by Di Cook
plotting individual values within multiple groups together with their means
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 data when some groups (or all groups) have few data points ! You may be wondering why to include such...
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Inferring the gender of the subjects from RNAseq BAM files
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 adjust your differential gene expression or splicing analysis. However, complete metadata are unfortunately ...
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Assessing the number of mapped reads in several bam files
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 that can be used for checking the number of aligned/mapped fragments in several bam files and dete...
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adhan package: retreiving and aligning the prayer times in R
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 be impossible to estimate or in other words it may simply not exist ! Some Muslim residents of those countries fo...
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These drinking glasses are too short!
These drinking glasses are too short! Some of my reinsurance and math teacher friends may remember that when I am out of town and having an adult beverage with friends, I have been known to stare at the drinking glass and say something like, “I don’t mean to be rude, but the glasses are certainly short here. They are much shorter than what ...
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Some different graph types in R
I don’t know about you, but I get tired of seeing column charts and pie charts. It’s not difficult to create a few more interesting chart types once in a while. Whether these are relevant for a particular audience and truly display your message is a different question. I wanted a really small dataset to experiment in R, so I used numbers of d...
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How do I count thee? Let me count the ways?
by Jerry Tuttle In Major League Baseball, a player who hits 50 home runs in a single season has hit a lot of home runs. Suppose I want to count the number of 50 homer seasons by team, and also the number of 50 homer seasons by New York Yankees. (I will count Maris and Mantle in 1961 as two.) Here is the data including Aar...
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Find the next number in the sequence
Between ages two and four, most children can count up to at least ten. If you ask your child, “What number comes next after 1, 2, 3, 4, 5?” they will probably say “6.” But to math nerds, any number can be the next number in a finite sequence. I like -14. Given a sequence of n real numbers f(x1), f(x2), f(x3), … , f(xn), t...
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Fixed effects vs. random effects for web browsing data – a simulation
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 several times from the same users (i.e., a panel data set). A first typical characteristi...
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Fixed vs. random effects for browsing data – a simulation
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 several times from the same users (i.e., a panel data set). A first typical character...
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