GetGeneMatrix: GetGeneMatrix get a gene matric for plotting genes by...

In MattPM/scglmmr: Sample-level Single-cell Generalized Linear Multilevel Models in R

GetGeneMatrix get a gene matric for plotting genes by celltypes statistic from pseudobulk model results e.g. using heatmap pheatmap or complexheatmap

Description

GetGeneMatrix get a gene matric for plotting genes by celltypes statistic from pseudobulk model results e.g. using heatmap pheatmap or complexheatmap

Usage

GetGeneMatrix(
  result.list,
  gene_subset = NULL,
  stat_for_matrix = "logFC",
  pvalfilter,
  logfcfilter
)

Arguments

result.list	the object returned by GetContrastResults or GetContrastResultsRaw
gene_subset	a preselected subset of genes as a vector, for example returned by GetLeadingEdgeFull. Defaults to the union of all fitted genes across cell types.
stat_for_matrix	defaults to logFC, the effect size. can be any of the columns returned by limma::topTable
pvalfilter	filter genes to retain in the matrix by the raw p values
logfcfilter	filter genes to retain in the matrix by the logFC

Value

a matrix

Examples

## Not run: 
le = scglmmr::GetLeadingEdgeFull(gsea.list = gsea1, padj.filter = 0.1, NES.filter = -Inf)
genesub = do.call(rbind, le) %$% gene %>% unique
mtx2 = scglmmr::GetGeneMatrix(result.list = res,
                              stat_for_matrix = "logFC",
                              gene_subset = genesub,
                              pvalfilter = -Inf,
                              logfcfilter = 0.1)

pheatmap::pheatmap(mtx2,
                   breaks =seq(from = 0, to = 2,length.out = 99),
                   filename = paste0(figpath,"LEgenes_heatmap.pdf"))

## End(Not run)

MattPM/scglmmr documentation built on April 26, 2024, 12:55 a.m.