robot_indexes_df: Returns dataframe with peptides which exhibit significant...

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

Returns dataframe with peptides which exhibit significant difference between two sets

Description

Function to help decide which peptides will be drawn on Robot plots.

Usage

robot_indexes_df(thP, th, replicates = 3, pvalue = 0.01, states, CI_factor = 1)

Arguments

thP	output of output_tcourse_proc() function. Raw data for procent deuteration for time courses
th	output of output_tcourse() function. Raw data for uptake deuteration for time courses
replicates	number of replicates in sample. Default set to 3.
pvalue	p-value cutoff. Default set up to 0.01
states	Protein states from the set. As default all states are chosen.
CI_factor	Multiplication factor for Critical Interval. Allows for more restrictive selection of Critial interval.

Value

Returns dataframe listing peptides that are significantly different between sets.

Examples

file_nm<-system.file("extdata", "All_results_table.csv", package = "HDXBoxeR")
tm_df<-output_tc(filepath=file_nm)
tmP_df<-output_tc(filepath=file_nm, percent=TRUE)

# more restictive peptide selection
robot_indexes_df(thP = tmP_df, th=tm_df, pvalue=0.001, CI_factor=3)

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