The following is a demonstration workflow for importing data from a
public repository. For an additional importing demonstration see
vignette("subsetting"). All the of examples presented here
are from previously published data where the raw data was analyzed on
each platform with basic settings for mass tolerance and PTMs.
ProteomeDiscoverer
Exporting the data requires some setup for the correct columns. This
is explained in vignette("importing").
library(dplyr)
library(tidyproteomics)
# download the data
url <- "https://data.caltech.edu/records/aevwq-2ps50/files/ProteomeDiscoverer_2.5_p97KD_HCT116_proteins.xlsx?download=1"
download.file(url, destfile = "./data/pd_proteins.xlsx")
# import the data
data_prot <- "./data/pd_proteins.xlsx" %>% import('ProteomeDiscoverer', 'proteins')MaxQuant
Exporting the data requires some setup for the correct columns. This
is explained in vignette("importing").
library(dplyr)
library(tidyproteomics)
# download the data
url <- "https://data.caltech.edu/records/aevwq-2ps50/files/MaxQuant_1.6.10.43_proteinGroups.txt?download=1"
download.file(url, destfile = "./data/mq_proteinGroups.txt")
# import the data
data_prot <- "./data/mq_proteinGroups.txt" %>%
import('MaxQuant', 'proteins')FragPipe
Exporting the data requires some setup for the correct columns. This
is explained in vignette("importing").
library(dplyr)
library(tidyproteomics)
# download the data
url <- "https://data.caltech.edu/records/aevwq-2ps50/files/FragPipe_19.1_combined_protein.tsv?download=1"
download.file(url, destfile = "./data/fp_combined_protein.tsv")
# import the data
data_prot <- "./data/fp_combined_protein.tsv" %>%
import('FragPipe', 'proteins')