liana_pipe: Liana Pipe which runs DE analysis and merges needed...

In saezlab/liana: LIANA: a LIgand-receptor ANalysis frAmework

Liana Pipe which runs DE analysis and merges needed information for LR inference

Description

Liana 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.

Value

Returns a tibble with information required for LR calculations downstream

saezlab/liana documentation built on Nov. 8, 2023, 11:53 a.m.