In ksong4/NetPhorce: Phosphoproteomics Network Analysis (NetPhorce)

knitr::opts_chunk$set(echo = TRUE)

This guide will help guide you to savely load your own data.

1. Correctly Loading MaxQuant Data

The original column names from MaxQuant contains spaces, which must be parsed as space for NetPhorce::confirmIntensityColumns() function to run, here we demonstrate one of the ways to correctly load the MaxQuant data to R environment via read_delim from tidyverse.

library(readr)
maxquantData = read_delim("<Path_to_Your_MaxQuant_File>", delim = "\t")

Once the data is loaded, please make sure you check on of the intensity column, i.e. "Intensity HT_0min_A___1", and make sure there is a space between "Intensity" and the TIME/REP/CON string. You can use the following script demo to check

knownColumnName = "Intensity HT_0min_A___1"
knownColumnName %in% colnames(maxquantData)

The output from the knownColumnName %in% colnames(maxquantData) need to return TRUE.

2. Time Units

Please make sure the time units you used for the analysis are based on the same unit. For example, if

ksong4/NetPhorce documentation built on March 24, 2023, 12:51 p.m.