To impute or not to impute scRNA-seq datasets?

Single-cell RNA-Seq methods, which sequence and barcode the transcripts within individual cells in a sample, hold enormous promise for understanding transcriptional networks in development and disease. Single-cell investigation of biological phenomena is taking the life sciences world by storm. For example, Science magazine selected single-cell methods as the 2018 “Breakthrough of the Year.”

Closer to home, our bioinformatics group here at the University of Iowa is also seeing a rapid increase in the number of scRNA-seq projects in the research pipeline. Yet with all of this interest and funding, scRNA-seq is still an emerging field with little agreement on best practices.

We see evidence of this when considering one of the main problems of scRNA-seq datasets: dropouts. ‘Dropouts’ are zero-values in the data arising from technical and biological noise. Often the dropout rate can reach up to 90% or more, degrading the ability of the analysis to detect fine structure in the data and low- and moderately expressed DE genes between cell types.

One way to combat this problem is to borrow information across genes within a sample and use that to predict imputed expression values for the missing genes. Another related approach is called data ‘smoothing,’ that attempts to lower the noise in observed values. There are several methods (MAGIC, scImpute, DrImpute, and SAVER) that have been published recently that attempt to do one or both of these approaches. While the authors of each method focus on the advantages of imputation, there can also be drawbacks caused by an increase in false-positives and loss of specificity.

A recent paper by Andrews and Hemberg address the potential drawbacks with imputation in a very concise and clear way using both simulated and real-world data. Figure 1 (below) from this paper shows very clearly the perils of doing imputation on false positive rates and spurious gene-gene correlations.

Performance on simulated scRNA-seq data

Figure 1A. Gene-gene correlations before (left) and after imputation with five methods (right). Red bars are highly-expressed DE genes, and blue bars are lowly-expressed DE genes. Gray bar are non-DE genes in this simulated dataset.

Somewhat dramatically, DrImpute and MAGIC introduce strong false positive correlations, while SAVER only strengthens existing correlations between lowly expressed DE genes. As you can see in part B of this figure below, parameter tuning also has a dramatic effect on the false positive rate in some cases. Increasing the k-neighbors for MAGIC and KNN methods increases smoothing and also false positives. SAVER and scImpute are relatively immune to changes in FPR with parameter space.

Figure 1B. False positive gene correlation rates as a function of algorithm parameters.

You can’t have your cake and eat it, too

In this next figure, the authors look at the trade-off between sensitivity and specificity in imputation methods on simulated datasets. It shows clearly that any improvements to sensitivity of DE gene detection come at a significant cost of specificity, and vice versa.

Detection of DE genes in simulated data.

The authors go on to show that on real data, every method including SAVER generates large numbers of false positives. In summary, imputation, while potentially promising, is limited owing to the lack of an independent reference (as in the case of GWAS imputation methods) to impute from. Since single-cell imputation methods rely only on the dataset itself, one cannot escape the sensitivity/specificity tradeoff and false-positive problem.

Gene expression boxplots with ggplot2

The ubiquitous RNAseq analysis package, DESeq2, is a very useful and convenient way to conduct DE gene analyses.  However, it lacks some useful plotting tools.   For example, there is no convenience function in the library for making nice-looking boxplots from normalized gene expression data.

There are other packages one can rely on, for example ‘pcaExplorer’, but I like a simple approach sometimes to plot just a couple of genes.  So below I show you how to quickly plot your favorite gene using only ggplot2 (there is no “one weird trick” though…):

As you can see above, first we must grab the normalized counts at the row corresponding with the Traf1 Ensembl ID using the ‘counts‘ function that operates on the ‘ddsTxi’ DESeqDataSet object.

In order to create a dataframe (well, a tibble to be specific) for plotting, we first create a list (‘m’) that combines the counts (as a numeric vector) and metadata group.  These two vectors will form the columns of the tibble for plotting, and we must give them names (i.e., “counts” and “group”) so the tibble conversion doesn’t complain.

The list, m, is then converted to a tibble with ‘as.tibble‘ and plotted with ggplot2, using an ‘aes(group,counts)‘ aesthetic plus a boxplot aesthetic.  The rest of the code is just modifying axis labels and tickmarks.  The final product looks like this:

Boxplot of normalized Traf1 expression in 5 different conditions (3 replicates each).

New “10 simple rules” paper for bioinformatics collaborations coming soon…

Excited to announce that I’ve been working with some fantastic computational biologists (that I met at ISMB2018) on a “10 simple rules” style paper for creating and promoting effective bioinformatics collaborations with wet-lab biologists.  We will leverage our many years of combined bioinformatics core experience to create these “10 simple rules.”

We will touch on:

–experiment planning and design.

–data management plans, data QC, and record keeping.

–avoiding batch effects and contamination.

–managing expectations and developing clear communications.

–handling low-quality data when things do go wrong.

Hope to have this out by the end of 2018…watch this space!

Artificial neural network classification of copy number variation, part 2

Recap:

Welcome to the second part of this post series on building artificial neural network models for copy number classification.  In the first part, I described the problem with interpreting copy-ratio plots to find clinically-relevant CNV events.  The data from targeted capture deep sequencing are noisy and biased, and finding clinically-relevant genotypes in genes that have CNVs requires the analyst to visualize the CNV event and assign a classification on the basis of experience and expert knowledge.

The LASSO model

Once my training data were in place (see part 1), I used a multiple linear regression LASSO model as a machine-learning benchmark.  I did this to determine whether a more powerful neural network model would be warranted.   The LASSO model uses an “L1” prior to perform feature selection, setting some coefficients to zero as warranted by the data.   There is ample precedent for applying this type of model in bioinformatics settings where the goal is maximize predictive power without overfitting.

I fit the LASSO to the data, with 33% held out for validation.  The best fit was obtained with the alpha parameter set to 0.001.  k-fold cross validation (where k=10 and alpha=0.001) yielded an accuracy of 76%.   These results are surprisingly good, given the complexity of the CNV signals in the noisy data.  Unfortunately, 76% accuracy is simply not good enough for an automated method that will be used to predict genotypes in clinical data.

The ANN model

Next, I decided to construct an artificial neural network model.  My goal was to keep the model as simple as possible, while reaching a very high classification accuracy needed for clinical work.   To that end I constructed a one hidden-layer model with 19 input nodes corresponding to the 19 copy-ratio probes in the CNV data.  The output layer contained five nodes, corresponding to the five classes of defined CNV event or other event (for example, a very distinct sequencing artifact that kept appearing in the data):

 

In between the input and output layers I constructed a 10-node hidden layer.   A one hidden-layer neural network is the simplest form of the ANN model, and I tried to keep the number of hidden-layer nodes to a minimum as well.  Specific details about the model, hyper-parameter tuning, and the code will be available in the near future when I put a pre-print of this work on biorxiv.

Model training and cross-validation

I trained the model on the 175 sample dataset and on a 350 sample “synthetic” dataset created by adding gaussian “noise” to the real data.  The results are shown below, across 250 training epochs.

When the ANN model was tested with 10-fold cross validation, the accuracy reached a level of 96.5% (+/- 5.4%).   This is obviously a big improvement on the LASSO model, and reaches a level of accuracy that is good enough for clinical pipelines (with the caveat that low confidence predictions will still be checked “by hand.”)

Below, I’m showing a sample of the model output (left) and ground truth (right) from the test data.  The numbers (and colors) of the boxes correspond to the model’s probability in that classification.  You can see that most CNV events are called with high probability, but several (yellow boxes) are called correctly but with lower probability.   One event (red box) is called incorrectly with high probability.

Conclusions and caveats

Going into this project, I had no idea if the ANN model would be able to make predictions on the basis of so few examples in the training set.  The classic examples you see about ANN/CNN models rely on handwriting training sets with 10,000 or more images.   So I was surprised when the model did very well with extremely limited training data.   Since this method was developed for a clinical pipeline, it can be improved as the pipeline generates new training data with each new patient sample.  We would need many thousands of samples through our “legacy” pipeline to see enough examples of the rare star allele events in CYP2D6 that we could then classify them.  That is why I limited my CNV calling to three star alleles.

The low confidence, true positive predictions concern me less than the high confidence false negative.  Missing a real CNV that has impact on CYP2D6 function and therefore clinical relevance is very dangerous.  This can lead to incorrect prescribing and adverse drug reactions for the patient.   I really want to understand why the method makes predictions like this, and how to fix it.  Unfortunately, I believe it will require a lot more training data to solve this problem and that is something I lack.

My goals for this project now are 1) to publish a preprint on biorxiv describing this work and 2) to obtain some additional training/test datasets.   Because our pharmacogenomics test is not generating the kind of volume we expected, I may have to look around for another gene with clinically-relevant CNV events to test this method further.   For example, we do have an NGS-based test of hearing and deafness genes with thousands of validated patient samples.  One gene, STRC, has relevant CNVs that are complex and require analyst visualization to detect.  This may be a good system for follow up refinement of this type of model.

Matataki, a new ultrafast read mapper: hope or hype?

tl;dr:  It’s only 2X faster than kallisto; a marginal, rather than “ultra” improvement.  If you’re already using kallisto in your pipelines there’s no reason to switch.   Now onto the blog post: 

Another RNA-seq read aligner

In July, a paper appeared in BMC Bioinformatics: “Matataki: an ultrafast mRNA quantification method for large-scale reanalysis of RNA-Seq data.”   The title seems to imply that Matataki is much faster than anything else out there.  After all, what does ‘ultrafast’ mean unless it’s in comparison to the next fastest method?  The authors claim it also solves a unique problem of large-scale RNA-seq reanalysis that can’t be solved any other way.  Is this true?  Let’s dive into the details and find out.

The authors point out in the introduction that the amount of publicly available RNA-seq data is increasing rapidly and that many would like to do large-scale reanalysis of these datasets.   Reanalysis (including realignment) is necessary because of the large batch effects of using different methods for alignment and quantification.

Although these alignment-free methods such as Sailfish, Kallisto, and RNA-Skim are much faster than the alignment-based methods, the recent accumulation of large-scale sequence data requires development of an even faster method for data management and reanalysis.

Counting unique k-mers

The method itself eschews traditional alignment for a k-mer based read counting approach.  This approach takes two steps:  build an index and quantify the reads against it.  Building the index requires the algorithm to search for all k-mers unique to a gene and also present in all isoforms of that gene (to avoid effects of differential expression of isoforms).  Quantification proceeds by matching the k-mers from a read with the unique k-mers in the index.  If there is only one indexed gene match from several k-mers (with a minimum cutoff set by the user) that read is assigned to the indexed gene.  If there is more than one match to several genes, the read is discarded.

If this sounds a lot like how kallisto operates under the hood, I would agree with you as would the authors:

Similar to Kallisto, our method uses k-mers that appear only once in a gene and quantifies expression from the number of unique k-mers.

Of course, kallisto creates a transcriptome de bruijn graph (tDBG) and uses compatibility classes to decide whether to skip k-mers while hashing a read.  Matataki does not use a tDBG and simply skips along a read using a fixed interval set by the user.   The code also skips the Expectation-Maximization (EM) step found in kallisto and focuses only on gene-level quantification.   These two novel approaches are what set Matataki apart from other pseudo-alignment algorithms, according to the authors.

But does it work?

Well, it appears to.  The authors start by reporting the performance of the method on simulated data using optimized parameters (I’ll discuss this below).  In Figure 2,  they describe the parameter tuning that led to those choices.  For parameter tuning the performance of Matataki on real data, the TPM values from an eXpress run on sample ERR188125 were taken as “ground truth.”  The choice of ‘eXpress’ as their benchmark for real-world dataset quantification is odd, given that eXpress is defunct and has been for some time.  It also takes orders of magnitude longer to complete than a method like sailfish or kallisto.

Fig 2. Comparison of TPM when k was varied. The x-axis shows the TPM values of eXpress, the y-axis shows the TPM values of our method, and the color indicates the indexed k-mer coverage of each gene when changing k from 16 to 56 with a step of 8

Going back to Figure 1 (below) and the performance on simulated data, we can observe accuracy similar to that of kallisto, RSEM, sailfish and other methods  (note that by using a scale from 0.93 to 0.99, the differences between the methods seem exaggerated).  The one simulated sample was created by RSEM from the real sample plus three other related samples.  So perhaps it’s not surprising that RSEM does the best in this comparison overall.

I think it’s important to remember as well that Matataki is being run on this simulated data with optimized parameters for this sample while the other methods are run with “default” parameters.   We don’t know how Figure 1a and 1b would change for other samples, other organisms, and other sequencing types (PE vs. SE, long vs. short, etc…)  It would be enlightening to find out.

Figure 1. Summary of the results using simulation data. a Spearman correlation coefficient with the expected expression and estimated expression values using each method. “Matataki” indicates the results of the proposed method, and “MatatakiSubset” indicates the results of the proposed method without uncovered genes. To compare the gene-level expression profile and transcript-level expression profile, the sum of TPM by each gene was calculated. b Means of absolute difference from the expected expression levels.

So how fast is ‘ultrafast’ anyway?

We finally get to the promised speed improvements near the end of the manuscript, only to find that the speedup relative to kallisto, a method that has been available publicly since at least 2015, is only 2-fold.  Yep, that’s it.  It’s only twice as fast.   This is an incremental improvement, but not a paradigm shift.  In fact, it shows how the leap from alignment to pseudo-alignment was in fact a paradigm shift when kallisto first came out.  It’s been three years and nothing has substantially improved on it.

Fig 3. CPU time comparison.

Limitations?

Finally, the authors end the paper with a section on ‘expected use-cases and limitations’ where they say that the method is only suitable for large-scale reanalysis and not for normal, turn-the-crank RNA-seq.

Nevertheless, Matataki is not suitable for common RNA-Seq purposes because other methods are sufficiently fast and provide better accuracy. For example, a single nucleotide substitution has larger effects in Matataki than in other methods, because even a single point substitution changes the k-mer for 2 k − 1 bases, which ultimately affects the number of k-mers in a transcript and calculation of the TPM value.

For reasons that I don’t understand, the authors promote this tool (which is only 2X faster than kallisto) as being for large-scale reanalysis, yet they performed no large-scale reanalysis to benchmark the tool.   Rather, they used it to perform normal RNA-seq as a benchmark, which they go on to say not to do in the wild.

To sum up, while a 2X speedup is useful, I see no reason to abandon kallisto to pseudoalign and quantify data when doing large scale reanalysis.   Unlike Matataki, kallisto is robust to read errors and it delivers transcript-level estimates that can be later summed to gene level, if you so desire.  It also provides bootstrapped estimates of technical variation, which helps to understand the biological variation as well.   And finally, kallisto integrates nicely with sleuth for DE testing and visualization.