liana_pipe | R Documentation |
Liana Pipe which runs DE analysis and merges needed information for LR inference
liana_pipe(
sce,
op_resource,
test.type = "wilcox",
pval.type = "all",
assay = "RNA",
assay.type = "logcounts",
verbose = TRUE,
base,
cell.adj = NULL
)
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 |
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. |
Returns a tibble with information required for LR calculations downstream
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