stat_activity_grouped: Compare activity differences between groups.

In hesselberthlab/scrunchy: Single Cell Reconstruction of Functional Heterogeneity

Description

Data is assumed to be tidy with a single grouping variable; all other variables are treated as activities to compare. Descriptive columns like cell_id should not be included.

Usage

stat_activity_grouped(tbl, group, complete = FALSE, ...)

Arguments

tbl	data from a SingleCellExperiment
group	variable for generating combinations
complete	If TRUE, generate complete group combinations (useful for e.g., matrix visulatization of p-values). Default is FALSE, generating unique groups combinations.
...	additional parameters to pass to calc_qvalues().

Details

Applies stats::wilcox.test() to unique pairs of groups for each measured variable. Adjusted p-values are calculated using qvalue::qvalue(). A ratio of activity in each group is reported; Inf values indicate that no activities were measured for the second group.

Value

tibble, sorted by q.value

• activity

• group

• group1

• ratio (ratio of the median signals in group over group1)

• p.value

• q.value

References

doi: 10.1038/nmeth.4612

Examples

x <- fsce_tidy[c("k_cluster", "Uracil_45", "riboG_44")]
stat_activity_grouped(x, group = k_cluster)

hesselberthlab/scrunchy documentation built on Nov. 11, 2019, 2:29 p.m.