pymol_script_significant_peptide_proc: Writes a text files with pymol scripts to list significant...

In mkajano/HDXBoxeR: Analysis of Hydrogen-Deuterium Exchange Mass-Spectrometry Data

Writes a text files with pymol scripts to list significant peptides

Description

Function write a script that can be used in pymol to color structure. Number of colors and corresponding to them ranges can be defined by user.

Usage

pymol_script_significant_peptide_proc(
  input_proc,
  input_up,
  path = "",
  ranges = c(-Inf, seq(-30, 30, by = 10), Inf),
  pv_cutoff = 0.01,
  replicates = 3,
  order.pep = TRUE
)

Arguments

input_proc	Dataframe with organized procent deuteration data. Input generated using output_tp(, percent=T) function.
input_up	Dataframe with organized deuteration uptake. Input generated using output_tp() function.
path	location where the Pymol scripts will be saved
ranges	ranges for coloring scheme. Default set to c(-Inf, seq(-30, 30, by=10), Inf)
pv_cutoff	p-value cutoff here set up to 0.01
replicates	number of replicates in sample. Default set to 3.
order.pep	flag allowing to either order peptide acccording to the peptide length (default), or to position in the protein sequence.

Value

pymol script with colors assigned per peptide

Examples

file_nm<-system.file("extdata", "All_results_table.csv", package = "HDXBoxeR")
a_up<- output_tp(file_nm)
a_proc<- output_tp(file_nm, percent=TRUE)
pymol_script_significant_peptide_proc(input_proc=a_proc,
input_up=a_up,  path=tempdir(),replicates=3, pv_cutoff=0.01,
ranges=c(-Inf,-40, -30,-20,-10, 0,10, 20,30,40, Inf), order.pep=TRUE)

mkajano/HDXBoxeR documentation built on April 23, 2024, 12:28 a.m.