programs: Find cell clusters and retrieve significant expresion...

In jlaffy/scalop: Single Cell Analysis Operations

Find cell clusters and retrieve significant expresion programs

Description

Cell clusters are filtered on the basis of size, their corresponding expression programs are subsequently filtered on the basis of number of genes with sufficiently high fold-change values and sufficiently small p-values, and lastly filtered on the basis of sufficiently low jaccard similarity between any two pairs of cell clusters, whereby the cell cluster with a larger number of significant genes is kept.

Usage

programs(
  m,
  groups = NULL,
  nsig1 = 50,
  nsig2 = 10,
  jaccard = 0.7,
  p = 0.01,
  lfc = log2(2),
  pmethod = "BH"
)

Arguments

m	expression matrix of genes by cells. not row-centered
groups	cell clusters provided and will not be computed from data.
nsig1	minimum number of genes with p-value 'p' to keep a cluster. Default: 50
nsig2	number of genes with p-value 'p'/10. Default: 10
jaccard	allowed jaccard similarity between clusters of cells. Default: 0.7
p	DEA adjusted p value for genes. Default: 0.01
lfc	DEA log2-FC value for genes. Default: log2(2)
pmethod	adjust method. Default: 'BH'

Value

The cell clusters, their gene expression profiles (all genes log2-foldchanges), their top DE genes (n = nsig1) and their p-values are all returned.

jlaffy/scalop documentation built on March 24, 2024, 9 a.m.