get_the_up_genes_for_group {celaref} | R Documentation

## get_the_up_genes_for_group

### Description

For the most overrepresented genes of the specified group in the test dataset, get their rankings in all the groups of the reference dataset.

### Usage

    get_the_up_genes_for_group(the_group, de_table.test, de_table.ref,
      rankmetric = "TOP100_LOWER_CI_GTE1")

### Arguments

`the_group` | The group (from the test/query experiment) to examine.
`de_table.test` | A differential expression table of the query experiment, as generated from `contrast_each_group_to_the_rest`
`de_table.ref` | A differential expression table of the reference dataset, as generated from `contrast_each_group_to_the_rest`
`rankmetric` | Placeholder for support of different ranking methods, but only the default supported. Omit.

### Details

This is effectively a subset of the reference data, 'marked' with the 'top' genes that represent the group of interest in the query data. The distribution of the rescaled ranks of these marked genes in each reference data group indicate how similar they are to the query group.

### Value

de_table.marked This will be a subset of de_table.ref, with an added column test_group set to the_group. If nothing passes the rankmetric criteria, NA.

### See Also

`contrast_each_group_to_the_rest` For prepraring the de_table.* tables. `get_the_up_genes_for_all_possible_groups` For running all query groups at once.

### Examples

    de_table.marked.Group3vsRef <- get_the_up_genes_for_group(
                                      the_group="Group3",
                                      de_table.test=de_table.demo_query,
                                      de_table.ref=de_table.demo_ref)

[Package celaref version 1.0.1 Index]