Performs test to detect changes in allelic ratio distribution across discrete groups.
group_mean.RdTests H0: all groups share the same mean vs H1: allelic ratio means are group-specific
Usage
group_mean(
a1_counts,
tot_counts,
metadata,
split.var = "group",
min_counts = 0,
min_cells = 5,
estimates,
estimates_group,
equalGroups = TRUE
)Arguments
- a1_counts
Integer matrix (genes x cells): allele-1 counts.
- tot_counts
Integer matrix (genes x cells): total counts. (same dimenstions and rownames as
a1_counts).- metadata
Metadata object containing cell level information (group identifier must be one of the column in the cell metadata)
- split.var
Name of the variable (group identifier) which will be used to split the cells.
- min_counts
Integer >= 0. Minimum reads per cell to include (default 0). Cells with a number of mapped reads less than min_counts are excluded from the estimation
- min_cells
Integer >= 1. Minimum number of cells per gene to fit (default 5). Genes with a number of cells less than min_cells are excluded from the estimation.
- estimates
Data frame from
correct_theta()- estimates_group
a list where each element is a data frame with group-level betabinomial estimates and corrected dispersion for each gene
- equalGroups
Controls for the equal number of cells between the groups (default TRUE)