mvGST (version 1.0.0)

pickOut: Returns gene sets in a cell of the results.table.

Description

pickOut returns a character vector with the Gene Ontology ID's of the gene sets with a particular significance profile for a certain contrast (the gene sets in one cell of the results.table of an mvGST object).

Usage

pickOut(mvgst, row, col = 1)

Arguments

mvgst

A mvGST object. mvGST$results.table must not be NULL.

row

The row of the desired profile.

col

The column of the desire contrast. Column refers to the levels of Var2, if Var2 was used. It is the number of the column after the 1, 0, -1 columns that show the profiles. Default value is 1.

Value

A data frame containing the ID's of the gene sets in the given row and column along with the GO descriptions of each gene set and the adjusted p-values for each contrast tested.

Details

To access the tutorial document for this package, type in R: vignette("mvGST")

References

Stevens, J. R., and Isom, S. C., 2012. "Gene set testing to characterize multivariately differentially expressed genes." Conference on Applied Statistics in Agriculture Proceedings, 24, pp. 125-137.

Mecham, D. S. (2014) "mvGST: Multivariate and Directional Gene Set Testing". MS Project, Utah State University, Department of Mathematics and Statistics. http://digitalcommons.usu.edu/gradreports/382/

Examples

data(mvGSTsamples)
# object obatoclax.mvGST returned by profileTable
obatoclax.mvGST

# returns the GO ID's from the cell in the third row and first column\
# (the column for cell line RS4) of the results.table of 
# the object returned by profileTable
pickOut(obatoclax.mvGST, 3, 1)

# See package vignette for larger examples with discussion: 
#    vignette("mvGST")