get_rankstat_table: get_rankstat_table

In MonashBioinformaticsPlatform/celaref: Single-cell RNAseq cell cluster labelling by reference

Description

Summarise the comparison of the specified query group against in the comparison in de_table.ref.marked - number of 'top' genes and their median rank in each of the reference groups, with reference group rankings.

Usage

get_rankstat_table(de_table.ref.marked, the_test_group)

Arguments

de_table.ref.marked	The output of get_the_up_genes_for_all_possible_groups for the contrast of interest.
the_test_group	Name of query group to test

Value

A tibble of query group name (test_group), number of 'top' genes (n), reference dataset group (group) with its ranking (grouprank) and the median (rescaled 0..1) ranking of 'top' genes (median_rank).

See Also

get_the_up_genes_for_all_possible_groups To prepare the de_table.ref.marked input.

Examples

# Make input
# de_table.demo_query <- contrast_each_group_to_the_rest(demo_query_se, "demo_query")
# de_table.demo_ref   <- contrast_each_group_to_the_rest(demo_ref_se,   "demo_ref")

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

get_rankstat_table(de_table.marked.query_vs_ref, "Group3")

MonashBioinformaticsPlatform/celaref documentation built on June 5, 2019, 11:35 a.m.