plots_vol_tp: Returns volcano plots for timepoints in the data frame

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

Returns volcano plots for timepoints in the data frame

Description

Returns volcano plots for each peptide. Critical interval is calculated according to #' Reliable Identification of Significant Differences in Differential Hydrogen Exchange-Mass Spectrometry Measurements Using a Hybrid Significance Testing Approach Tyler S. Hageman and David D. Weis Analytical Chemistry 2019 91 (13), 8008-8016 DOI: 10.1021/acs.analchem.9b01325 calculations for alpha 0.99 pvalues calculated using Welch t-test.

Usage

plots_vol_tp(df, replicates = 3, pv_cutoff = 0.01, cola)

Arguments

df	output from functions output_tp
replicates	number of replicates in set as default set to 3.
pv_cutoff	p-value cutoff here set up to 0.01
cola	color pallette for different Protein States. As default Paired pallette from color.Brewer is used.

Value

volcano plots

Examples

file_nm<-system.file("extdata", "All_results_table.csv", package = "HDXBoxeR")
a<- output_tp(file_nm)
plots_vol_tp(df=a, replicates=3, cola=c(1:4), pv_cutoff=0.01 )
plots_vol_tp(df=a, pv_cutoff=0.05)

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