IRProfiler – a software toolbox for high throughput immune receptor profiling

BMC Bioinformatics

Table 4 Results of theoretical and experimental execution time estimation (extracted independently) for the developed tools

Index	Tool	O(·)	R ²
1	Data filtering	O(n)	0.999808
2	Clonotype diversity and expression	O(n)	[0.999508, 0.999717]
3	Gene usage	O(n)	[0.976990, 0.981139]
4	Public clonotypes	O(m·n²)	[0.976313, 0.996352]
5	Exclusive clonotypes	O(n²)	[0.937594, 0.958152]
6	Gene usage comparison	O(m·n²)	[0.834540, 0.864164]

For the theoretical estimation (3rd column), n is the number of input receptor reads or clonotypes and m is the number of input repertoire datasets. For the experimental estimation (4th column), exactly 2 input datasets have been assumed for the 4th–6th tools. The 4th column includes the coefficient of determination values (R²) assuming a first (1st-3rd tool) and second (4th–6th tool) order polynomial model of the execution time; whenever multiple alternative clonotype definitions or gene subgroups are supported by a tool, ranges of values are reported

ISSN: 1471-2105