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bbbq_1_smart

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`develop`

The article 'Transmembrane helices are an overlooked and evolutionarily conserved source of major histocompatibility complex class I and II epitopes', by Bilderbeek, Baranov, van den Bogaart and Bianchi.

Bilderbeek, Richèl JC, et al. "Transmembrane helices are an overlooked and evolutionarily conserved source of major histocompatibility complex class I and II epitopes." bioRxiv (2021).

@article{bilderbeek2021transmembrane,
  title={Transmembrane helices are an overlooked and evolutionarily conserved source of major histocompatibility complex class {I} and {II} epitopes},
  author={Bilderbeek, Richèl JC and Baranov, Maxim and van den Bogaart, Geert and Bianchi, Frans},
  journal={bioRxiv},
  year={2021},
  publisher={Cold Spring Harbor Laboratory}
}

Build

make

File structure

`[target]_[percentage]_counts.csv`

`haplotype`	`name`	`n_binders`	`n_binders_tmh`	`n_spots`	`n_spots_tmh`
h1	p1	11	5	100	20
h1	p2	12	4	10	2

Note that:

n_spots and n_spots_tmh can vary, due to MHC class-dependent epitope lengths.
we only keep track of the membrane proteins, n_spots_tmh will thus be always greater than zero

Rscript create_all_counts_per_proteome.R [target] [percentage]
Rscript create_all_counts_per_proteome.R human 5

`counts_[percentage].csv`

`target`	`haplotype_id`	`protein_id`	`n_binders`	`n_binders_tmh`	`n_spots`	`n_spots_tmh`
covid	h1	p1	11	5	100	20
covid	h1	p2	12	6	101	20

Note that:

we only keep track of the membrane proteins, n_spots_tmh will thus be always greater than zero

Rscript merge_all_counts.R [percentage]
Rscript merge_all_counts.R 5

`table_tmh_binders_mhc[mhc_class].csv`

Pretty-printed version

`haplotype`	`covid`	`human`
HLA-A*01:01	38.46 (5/13)	25.00 (5/20)
HLA-B*39:01	100.00 (2/2)	58.33 (14/24)
HLA-B*40:02	55.56 (5/9)	29.17 (7/24)

Note that:

up so far, we only kept track of the membrane proteins. Here we correct the percentages to include the full proteome again

Rscript create_table_tmh_binders_mhc.R mhc1
Rscript create_table_tmh_binders_mhc.R mhc2

Figures

Note that:

up so far, we only kept track of the membrane proteins. Here we correct the percentages to include the full proteome again