wilcoxExt: Extension on Pairwise Mann Whitney Wilcoxon Test for...

In Wancen/airpart: Differential cell-type-specific allelic imbalance

Extension on Pairwise Mann Whitney Wilcoxon Test for partitioning

Description

Extends the Pairwise Mann Whitney Wilcoxon Test by combining hierarchical clustering for partition.

Usage

wilcoxExt(
  sce,
  genecluster,
  threshold,
  adj.matrix,
  p.adjust.method = "none",
  ncores = NULL,
  ...
)

Arguments

sce	A SingleCellExperiment containing assays ("ratio", "counts") and colData "x"
genecluster	which gene cluster result want to be returned. Usually identified interesting gene cluster pattern by summaryAllelicRatio
threshold	a vector with candidate thresholds for raw p-value cut-off. Default is 10^seq(from=-2,to=-0.4,by=0.2). For details please see vignette
adj.matrix	an adjacency matrix with 1 indicates cell states allowed to be grouped together, 0 otherwise.
p.adjust.method	method for adjusting p-values (see p.adjust). Can be abbreviated
ncores	A cluster object created by makeCluster. Or an integer to indicate number of child-processes (integer values are ignored on Windows) for parallel evaluations
...	additional arguments to pass to wilcox.test.

Value

A matrix grouping factor partition and the significant cut-off threshold are returned in metadata "partition" and "threshold". Partation also stored in colData"part". Note we recommend the returned "threshold" is not at the ends of input "threshold".

Examples

library(S4Vectors)
sce <- makeSimulatedData()
sce <- preprocess(sce)
sce <- geneCluster(sce, G = seq_len(4))
sce_sub <- wilcoxExt(sce, genecluster = 1)
metadata(sce_sub)$partition
metadata(sce_sub)$threshold

# Suppose we have 4 cell states, if we don't want cell state 1
# to be grouped together with other cell states
adj.matrix <- 1 - diag(4)
colnames(adj.matrix) <- rownames(adj.matrix) <- levels(sce$x)
adj.matrix[1, c(2, 3, 4)] <- 0
adj.matrix[c(2, 3, 4), 1] <- 0
thrs <- 10^seq(from = -2, to = -0.4, by = 0.1)
sce_sub <- wilcoxExt(sce,
  genecluster = 1, threshold = thrs,
  adj.matrix = adj.matrix
)
metadata(sce_sub)$partition

Wancen/airpart documentation built on March 12, 2023, 11:53 a.m.