get_the_up_genes_for_group: get_the_up_genes_for_group

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

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", n = 100)

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	Specifiy ranking method used to pick the 'top' genes. The default 'TOP100_LOWER_CI_GTE1' picks genes from the top 100 overrepresented genes (ranked by inner 95 work best for distinct cell types (e.g. tissue sample.). 'TOP100_SIG' again picks from the top 100 ranked genes, but requires only statistical significance, 95 clusters (e.g. PBMCs).
n	For tweaking maximum returned genes from different ranking methods. Will change the p-values! Suggest leaving as default unless you're keen.

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)

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