metaprograms: Compute Metaprograms

In jlaffy/scalop: Single Cell Analysis Operations

Compute Metaprograms

Description

programs and profiles are the lists of gene sets and DE profiles that were derived from intra-tumour cell clusters. These are integrated, according to the metaclusters clustering, into a final list of metaprograms; one per metacluster.

Usage

metaprograms(
  programs,
  profiles,
  m,
  metaclusters,
  samples = NULL,
  freq.cutoff = 3,
  order.priority = c("freq", "lfc"),
  return.data = FALSE
)

Arguments

programs	list of differentially expressed genes in each group/cell cluster
profiles	list of differential expression profiles for all genes in each group/cell cluster
m	matrix of genes by cells
metaclusters	list of program metaclusters
samples	character vector of unique sample names. Default: readRDS("samples_2020-03-01.rds")
order.priority	order by 'freq' first or 'lfc' first. Default: 'freq'
freq	minimum number of metacluster-specific sample-specific programs a gene must appear in. Default: 3

Details

DETAILS

Value

if return.data = F, just the list of metaprograms. Else, the list of metaprograms, and the dataframe of metacluster-, sample- and gene- specific LFC and freq values.

See Also

melt select,mutate,join,group_by,distinct,filter,arrange

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