get_the_up_genes_for_all_possible_groups {celaref} | R Documentation

## get_the_up_genes_for_all_possible_groups

### Description

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

### Usage

    get_the_up_genes_for_all_possible_groups(de_table.test, de_table.ref,
      rankmetric = "TOP100_LOWER_CI_GTE1")

### Arguments

`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 groups 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.

This function is simply a conveinent wrapper for `get_the_up_genes_for_group` that merges output for each group in the query into one table.

### Value

de_table.marked This will alsmost be a subset of de_table.ref, with an added column test_group set to the query groups, and test_dataset set to test_dataset_name.

If nothing passes the rankmetric criteria, a warning is thrown and NA is returned. (This can be a genuine inability to pick out the representative 'up' genes, or due to some problem in the analysis)

### See Also

`get_the_up_genes_for_group` Function for testing a single group.

### Examples

    de_table.marked.query_vs_ref <- get_the_up_genes_for_all_possible_groups(
       de_table.test=de_table.demo_query ,
       de_table.ref=de_table.demo_ref )

[Package celaref version 1.0.1 Index]