output_prep {HDXBoxeR}

Prepares output with HDX-MS data for publications

Description

Format prepared based of example from: Masson, G.R., Burke, J.E., Ahn, N.G. et al. Recommendations for performing, interpreting and reporting hydrogen deuterium exchange mass spectrometry (HDX-MS) experiments. Nat Methods 16, 595–602 (2019). https://doi.org/10.1038/s41592-019-0459-y It generates csv file in format ready for publication of the data.

Usage

output_prep(filepath, output_name, states, replicates, times, percent = FALSE)

Arguments

filepath

filepath to the input file. Input file is All_results table from HDX_Examiner, where all the fields are marked for export.

output_name

Name of output file. It has to be csv file

states

function allows to choose what states should be used for analysis. Default all states are used.

replicates

number of replicates to be used in analysis. The function takes number of replicates up to specified number. If no argument provided number maximal common number of replicates it used.

times

lists the deuteration times to be used in analysis. Default all states used.

percent

return either uptake or percent deuteration, default=FALSE, return uptake

Value

Returns&saves data.frame in format that is accepted for the publications.

Examples

file_nm<-system.file("extdata", "All_results_table.csv", package = "HDXBoxeR")
output_prep(filepath=file_nm, output_name=tempfile())