pickOut {mvGST} | R Documentation

## 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.

### Details

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

### 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.

### Author(s)

John R. Stevens and Dennis S. Mecham

### 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")

[Package mvGST version 1.12.2 Index]