Gini coefficient TCR repertoire

Question

[Lucy]

Hi,

I would like to calculate the Gini coefficient for my TCR repertoire data. I have seen that this can be calculated using the DescTools and ineq packages in R, however from the package documentation, I am unclear what input is required in the context of TCR repertoire data.

Is anyone able to help with this?

Best wishes,

Lucy

Answer 1

[Kevin Blighe]

Hi,

The Gini coefficient is used in many diverse ways, it seems.

In the context of TCR-seq, you could use it to check for 'inequality' among clonotypes on a per sample or group (condition) basis.

Which data have you got, currently?

Kevin

[Lucy]

Hi Kevin,

Thank you - yes I have paired scTCR-seq data and I would like to compare the clonality of the alpha vs. beta chain.

Best wishes,

Lucy

[Kevin Blighe]

I see. The function in DescTools appears to just literally accept, at minimal, a vector of values, like c(45,33,67, ..., 45). I suppose that, technically, a Gini coefficient can be calculated from this, where each number represents usage (normalised read count?) of a particular clonotype.

[Lucy]

Based on this vignette (https://www.statology.org/gini-coefficient-in-r/), I think the required input would be the clonotype assignment for each cell rather than the abundances.