6.1 ArchR’s LSI Implementation

ArchR implements a few different LSI implementations and we have benchmarked many of these methods across multiple different test data sets. ArchR’s default LSI implementation is related to the method introduced by Timothy Stuart in Signac, which uses a term frequency that has been depth normalized to a constant (10,000) followed by normalization with the inverse document frequency and then log-transforming the resultant matrix (aka log(TF-IDF)).

One of the key inputs to LSI dimensionality reduction is the starting matrix. Thus far, the two main strategies in scATAC-seq have been to (1) use peak regions or (2) genome-wide tiles. However, using peak regions for LSI is inherently challenging because we do not have clusters or cluster-specific peaks prior to dimensionality reduction. Moreover, calling peaks on aggregated cells prior to clustering obscures cell type-specific peaks. Moreover, any union peak set will change when new samples are added to an experiment, making this strategy less stable. The second strategy, using genome-wide tiles, mitigates these issues by using a consistent and unbiased feature set (genome-wide tiles). However, a genome-wide tile matrix of all cells by all regions can become prohibitively large. For this reason, most implementations use tiles that are greater than or equal to 5 kilobases in size. This drastically reduces the resolution of the approach because most accessible regions are only a few hundred basepairs long.

Because of the way that Arrow files are designed, ArchR is able to perform LSI very rapidly using genome-wide 500-bp tiles. This solves the problem of resolution and allows for the identification of clusters prior to calling peaks. The challenge is that 500-bp bins generate around 6 million features to be included in the cell by tile matrix. While ArchR is able to read this large amount of data into R by chunking the relevant matrices, we have also implemented an “estimated LSI” approach that performs the initial dimensionality reduction on a subset of the total cells. This estimated LSI approach has two main utilities - (i) it speeds up dimensionality reduction and (ii) as you decrease the number of cells used in the intial dimensionality reduction, this decreases the granularity of the data. This reduction in granularity can be used to your advantage to reduce batch effects in your data. However, it can also obscure true biology so estimated LSI approaches should be used under close manual supervision.