mutscan—a flexible R package for efficient end-to-end analysis of multiplexed assays of variant effect data

Table 2 Overview of deep mutational scanning data sets used in this study

Data set	Number of replicates	Library type	Molecule	Activity measured	Total number of reads (Mio.)
Diss_FOS [6]	3	Individual locus	Protein	PPI	262.4
Diss_FOS_JUN [6]	3	Two paired loci	Protein	PPI	245.7
Bolognesi_TDP43_290_331 [11]	3	Individual locus	Protein	Aggregation	180.0
Li_tRNA_sel30 [25]	5	Individual locus	RNA	Fitness	511.4 (1685.7^a)

^aIn the Li_tRNA_sel30 data set, a single-input replicate is paired with multiple output replicates. While the modular design of mutscan allows to process this shared input replicate just once, DiMSum (with the design used here, in agreement with [20]) requires it to be processed repeatedly, once for each selected replicate, which increases the number of processed read pairs from 511.4 to 1685.7 Mio

ISSN: 1474-760X