Description Usage Arguments Value Author(s) Examples
subset molecular interaction data (cleaned MITAB format in a data.table object) with a list of interactors
1 2 3 |
data |
a list contatining PPI data as generated by |
directory |
where to find / keep PPI data (arg for |
Interaction_detection_methods |
arg for |
Identification_method |
arg for |
PMIDs |
arg for |
inverse_filter |
logical, inverse filtering criteria |
data_name |
to be displayed on plot |
data.table to be ggplotted to compare viral and human protein degree distributions
Vitalii Kleshchevnikov
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 | {
# Load data. This can be done internally by humanViralDegree(),
# however, it takes time (minutes) so it's recommended to load data separately
# if it will be used multiple times
HumanViralPPI = loadHumanViralPPI(directory = "./data_files/")
# prepare all data for the degree distribution analysis
degree_distributions = humanViralDegree(data = HumanViralPPI,
directory = "./data_files/", data_name = "Full IntAct")
# prepare two-hybrid data for the degree distribution analysis
degree_distributions = humanViralDegree(data = HumanViralPPI,
directory = "./data_files/", Interaction_detection_methods = "MI:0018",
data_name = "two-hybrid data")
# prepare AP-MS data for the degree distribution analysis
degree_distributions = humanViralDegree(data = HumanViralPPI,
directory = "./data_files/", Interaction_detection_methods = "MI:0004",
Identification_method = "MI:0433", PMIDs = NULL, inverse_filter = F,
data_name = "AP-MS data")
# to see if viral-interacting human proteins are special in the human network,
# look at the Vidal published and unpublished datasets (only human-human network
# is modified (data for the top 2 plots))
degree_distributions = humanViralDegree(data = HumanViralPPI,
directory = "./data_files/", PMIDs = c("25416956", "unassigned1304"),
data_name = "Vidal published and unpublished")
# to see if viral-interacting human proteins are special in the human network,
# do the same for Matthias Mann 2015 paper dataset
degree_distributions = humanViralDegree(data = HumanViralPPI,
directory = "./data_files/", PMIDs = "26496610",
data_name = "Matthias Mann 2015 paper")
}
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.