HDXBoxeR (version 0.0.2)

pymol_script_significant_residue_proc: 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 colored by average procent_deuteration from the significant peptides per residues.

Usage

pymol_script_significant_residue_proc(
  input_up,
  input_proc,
  path = "",
  ranges = c(-Inf, seq(-30, 30, by = 10), Inf),
  pv_cutoff = 0.01,
  replicates = 3
)

Value

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

Arguments

input_up

Dataframe with organized deuteration uptake. Input generated using output_tp() function.

input_proc

Dataframe with organized procent deuteration data. Input generated using output_tp_proc() 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.

Examples

# \donttest{
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_residue_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))
# }