Liana Pipe which runs DE analysis and merges needed information for LR inference
Source:R/liana_pipe.R
liana_pipe.RdLiana Pipe which runs DE analysis and merges needed information for LR inference
Usage
liana_pipe(
sce,
op_resource,
test.type = "wilcox",
pval.type = "all",
assay = "RNA",
assay.type = "logcounts",
verbose = TRUE,
base,
cell.adj = NULL
)Arguments
- sce
SingleCellExperiment Object
- op_resource
resource tibble obtained via liana::select_resource
- test.type
String specifying the type of pairwise test to perform - a t-test with
"t", a Wilcoxon rank sum test with"wilcox", or a binomial test with"binom".- pval.type
A string specifying how p-values are to be combined across pairwise comparisons for a given group/cluster.
- assay
assay to be used ("RNA" by default)
- assay.type
- the type of data to be used to calculate the means (logcounts by default), available options are: "counts" and "logcounts"
- verbose
logical for verbosity
- base
base for conversion from log-tranformed ~CPM back to ~CPM.
- cell.adj
cell adjacency tibble/dataframe /w weights by which we will `multiply` the relevant columns. Any cell pairs with a weights of 0 will be filtered out. Note that if working with LIANA's default methods, we suggest weights >= 0 & =< 1. This ensure that all methods' score will be meaningfully weighed without changing the interpretation of their scores, thus allow one to filter SCA, rank NATMI, etc.