hydrophobicity_distribution: Determines the hydrophobicity distribution of all peptides in...

In richelbilderbeek/bbbq: The Bilderbeek Bianchi and Bogaart Question

Determines the hydrophobicity distribution of all peptides in the human proteome as well as all peptides overlapping with transmembrane helices.

Description

Inputs: * proteome_as_data_filename * tmh_9mers_as_data_filename * kyte_doolittle_scale_as_data_filename

Usage

hydrophobicity_distribution(
  proteome_as_data_filename,
  tmh_9mers_as_data_filename,
  kyte_doolittle_scale_as_data_filename,
  proteome_9mer_hydrophobicity_as_data_filename
)

Arguments

proteome_as_data_filename	filename to store the proteome in R data format, for example 'work/proteome.Rdata'
tmh_9mers_as_data_filename	filename to store per TMH protein, the indices at which it is TMH, in R data format. for example 'work/tmh.9mers.Rdata'
kyte_doolittle_scale_as_data_filename	filename that stores the Kyte-Doolittle scale of hydrophobicity, for example 'data/kyte.doolittle.scale.Rdata'
proteome_9mer_hydrophobicity_as_data_filename	filename to store the proteome 9-mer hydrophobicities in R data format, for example 'work/proteome.9mer.hydrophobicity.Rdata'

Details

Output: * proteome_9mer_hydrophobicity_as_data_filename

Author(s)

Richèl J.C. Bilderbeek, adapted from Johannes Textor

richelbilderbeek/bbbq documentation built on July 27, 2023, 2:15 a.m.