cluster_logistic_test: Test clusters for differential usage

In CellaRepertorium: Data structures, clustering and testing for single cell immune receptor repertoires (scRNAseq RepSeq/AIRR-seq)

Description

Typically one will want to stratify by chain by calling cluster_test_by, as this will calculate the number of cell "trials" separately depending on the chain recovered.

Usage

cluster_test_by(ccdb, fields = "chain", tbl = "cluster_tbl", ...)

cluster_logistic_test(
  formula,
  ccdb,
  filterset = cluster_filterset(),
  contig_filter_args = TRUE,
  tie_break_keys = c("umis", "reads"),
  add_cluster_tbl = FALSE,
  keep_fit = FALSE,
  fitter = glm_glmer,
  silent = FALSE
)

Arguments

ccdb	ContigCellDB()
fields	character naming fields in tbl
tbl	one of contig_tbl, cell_tbl or cluster_tbl
...	passed to cluster_logistic_test
formula	the right-hand side of a glmer or glm-style formula.
filterset	a call to cluster_filterset() that will be used to subset clusters.
contig_filter_args	an expression passed to dplyr::filter(). Unlike filter, multiple criteria must be & together, rather than using commas to separate. These act on ccdb$contig_tbl
tie_break_keys	(optional) character naming fields in contig_tbl that are used sort the contig table in descending order. Used to break ties if contig_filter_args does not return a unique contig for each cluster
add_cluster_tbl	logical should the output be joined to the cluster_tbl?
keep_fit	logical as to whether the fit objects should be returned as a list column
fitter	a function taking arguments formula, data, is_mixed and keep_fit that is run on each cluster. Should return a tibble or data.frame
silent	logical. Should warnings from fitting functions should be suppressed?

Value

table with one row per cluster/term.

Functions

• cluster_test_by: split ccdb and conduct tests within strata

Examples

library(dplyr)
data(ccdb_ex)
ccdb_ex = cluster_germline(ccdb_ex)
trav1 = filter(ccdb_ex$cluster_tbl, v_gene == 'TRAV1')
cluster_logistic_test(~pop + (1|sample), ccdb_ex,
filterset = cluster_filterset(white_list= trav1))
# Fixed effect analysis of each cluster, by chain
prev4 = ccdb_ex$contig_tbl %>% group_by(cluster_idx) %>%
summarize(n()) %>% filter(`n()`>= 4)
cluster_test_by(ccdb = ccdb_ex, fields = 'chain',
tbl = 'cluster_tbl', formula = ~ pop, filterset = cluster_filterset(white_list= prev4))

CellaRepertorium documentation built on Nov. 8, 2020, 7:48 p.m.