pickOut: Returns gene sets in a cell of the 'results.table'.
In mvGST: Multivariate and directional gene set testing

Description Usage Arguments Details Value Author(s) References Examples

View source: R/pickOut.R

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).

1	pickOut(mvgst, row, col = 1)

`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.

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

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.

John R. Stevens and Dennis S. Mecham

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/

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")