cluego: ClueGO via API

In qzhang503/proteoQ: Processing and Informatic Analysis of Mass Spectrometrirc Data

ClueGO via API

Description

cluego sends anal_prnTrend findings in, e.g. Protein_Trend_[...].txt etc. to ClueGO via API.

Usage

cluego(
  df2 = "Protein_Trend_Z_nclust5.txt",
  species = c(human = "Homo Sapiens"),
  n_clust = 3L
)

Arguments

df2	Character string; the name of a secondary data file from anal_prnTrend, such as Protein_Trend_Z_nclust6.txt etc.
species	Named character string . The default is c(human = "Homo Sapiens"). In this example, human is the value that can be found under the species column in a Trend result table and "Homo Sapiens" is the corresponding species name in ClueGO.
n_clust	Numeric vector; the cluster ID(s) corresponding to anal_prnTrend for visualization.

Examples

# Make sure CytoSpace is opened, and 
# yFiles layouts and ClueGO plug-in are installed.

# Human
cluego(
  df2 = Protein_Trend_Z_nclust5.txt, 
  species = c(human = "Homo Sapiens"), 
  n_clust = c(3, 5)
)

# Mouse
cluego(
  df2 = Protein_Trend_Z_nclust5.txt, 
  species = c(mouse = "Mus Musculus"), 
  n_clust = c(3:4)
)

qzhang503/proteoQ documentation built on Dec. 14, 2024, 12:27 p.m.