pymol_script_average_residue: 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 residues.

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. Residues are being colored by average uptake values from the significant peptides per residues.

Usage

pymol_script_average_residue(
  df,
  path = "",
  ranges = c(-Inf, seq(-30, 30, by = 10), Inf),
  pv_cutoff = 0.01,
  replicates = 3
)

Arguments

df	output from functions output_tp
path	output folder location
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.

Value

pymol script with residues colored based on average of uptake per residue.

Examples

file_nm<-system.file("extdata", "All_results_table.csv", package = "HDXBoxeR")
a<- output_tp(file_nm)
pymol_script_average_residue(df=a, replicates=3, pv_cutoff=0.01,
ranges=c(-Inf,-40, -30,-20,-10, 0,10, 20,30,40, Inf), path=tempdir() )
pymol_script_average_residue(df=a,  path=tempdir())

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