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