annotate.gs: Summary annotation information of a gene set

Description Usage Arguments Value Author(s) See Also Examples

View source: R/GIS.R

Description

Retrive variables/features (genes) mapped to the annotated data sets in a gene set. Also returns the the information about presence and absence of a feature for a specific data set.

Usage

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  annotate.gs(mgsa, gs)

Arguments

mgsa

An object of class mgsa-class or moa.sup-class.

gs

The name of a geneset

Value

This function returns a data.frame. The first column shows the name of features. The last column is for the count of how many data sets has the corresponding features. Columns in the middle contains logical value indicating whether a feature is presented in a particular data set.

Author(s)

Chen Meng

See Also

see GIS

Examples

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  # library(mogsa)
  # loading gene expression data and supplementary data
  data(NCI60_4array_supdata)
  data(NCI60_4arrays)
  mgsa <- mogsa(x = NCI60_4arrays, sup=NCI60_4array_supdata, nf=9,
                proc.row = "center_ssq1", w.data = "inertia", statis = TRUE)
  allgs <- colnames(NCI60_4array_supdata[[1]])
  annotate.gs(mgsa, allgs[1])

mengchen18/mogsa documentation built on Nov. 23, 2017, 1:57 a.m.