get_the_up_genes_for_group {celaref} | R Documentation |
For the most overrepresented genes of the specified group in the test dataset, get their rankings in all the groups of the reference dataset.
get_the_up_genes_for_group(the_group, de_table.test, de_table.ref, rankmetric = "TOP100_LOWER_CI_GTE1")
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
|
de_table.ref |
A differential expression table of the reference
dataset, as generated from
|
rankmetric |
Placeholder for support of different ranking methods, but only the default supported. Omit. |
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.
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.
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.
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)