deCS.fisher: Cell type enrichment analysis by Fisher's exact test
In GuangshengPei/deCS: Cell type enrichment analysis

View source: R/deCS.R

deCS.fisher

R Documentation

Cell type enrichment analysis by Fisher's exact test

Description

Cell type enrichment analysis by Fisher's exact test for user provide human gene list.

Usage

deCS.fisher(markers_list, ref_panel, type = "score", ref_panel_markers_ratio = 0.05, top_n = 3, p.adjust.methods = "BH", label = "ratio", 
intersection_threshold = 0.1, p_threshold = 0.05, cell_type_threshold = 0, plot_figure = TRUE)

Arguments

`markers_list`	Gene list with at least two columns with name "cluster" (cell type) and "gene" (marker gene list).
`ref_panel`	Gene cell type specific t-score or z-score matrix, can be loaded by data(ref_panel), ref_panel = c("BlueprintEncode_main", "BlueprintEncode_fine", "Human_cell_landscape", "Human_cell_atlas_of_fetal", "DICE_main", "DICE_fine", "MonacoImmune_main", "MonacoImmune_fine", "CellMatch").
`type`	When reference is t-score or z-score matrix, specifify type = "score", when reference is cell type-marker gene list, specifify type = "list".
`ref_panel_markers_ratio`	The threshold to define cell type-specific genes (with top t-score or z-score), the default value is 0.05.
`top_n`	deCS result will list top n most similar cell types, the default value is 3.
`p.adjust.methods`	p.adjust.method, c("holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none").
`label`	Calculate the gene intersection ratio between query and reference CSGs genes, specifify label = "ratio"; or calculate the gene intersection count, specifify label = "count".
`intersection_threshold`	The minimum correlation intersection threshold for cell type annotation, the default value is 0.1. When label = "count", please provide a larger number, e.g. intersection_threshold = 10. Cells failed to pass the threshold will be regarded as "Undetermined cells".
`p_threshold`	The minimum p-value for cell type annotation, the default value is 0.05. Cells failed to pass the threshold will be regarded as "Undetermined cells".
`cell_type_threshold`	Figure plot only, only show significant correlated cell types, the default value is 0.
`plot_figure`	Plot figure or not, the maximum query cell number is 100, the default value is TRUE.