HDXBoxeR (version 0.0.2)

pymol_script_significant_peptide_proc: 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
)

Value

pymol script with colors assigned per peptide

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.

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_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)
# }