normalize_gene_activities: Normalize gene activities

In cole-trapnell-lab/cicero: Predict cis-co-accessibility from single-cell chromatin accessibility data

Normalize gene activities

Description

Normalize the output of build_gene_activity_matrix. Input is either one or multiple gene activity matrices. Any gene activities to be compared amongst each other should be normalized together.

Usage

normalize_gene_activities(activity_matrices, cell_num_genes)

Arguments

activity_matrices	A gene activity matrix, output from build_gene_activity_matrix, or a list of gene activity matrices to be normalized together.
cell_num_genes	A named vector of the total number of accessible sites per cell. Names should correspond to the cell names in the activity matrices. These values can be found in the "num_genes_expressed" column of the pData table of the CDS used to calculate the gene activity matrix.

Value

Normalized activity matrix or matrices.

Examples

  data("cicero_data")
  data("human.hg19.genome")
  sample_genome <- subset(human.hg19.genome, V1 == "chr18")
  sample_genome$V2[1] <- 100000
  input_cds <- make_atac_cds(cicero_data, binarize = TRUE)
  input_cds <- detectGenes(input_cds)
  input_cds <- reduceDimension(input_cds, max_components = 2, num_dim=6,
                               reduction_method = 'tSNE',
                               norm_method = "none")
  tsne_coords <- t(reducedDimA(input_cds))
  row.names(tsne_coords) <- row.names(pData(input_cds))
  cicero_cds <- make_cicero_cds(input_cds,
                                reduced_coordinates = tsne_coords)
  cons <- run_cicero(cicero_cds, sample_genome, sample_num=2)

  data(gene_annotation_sample)
  gene_annotation_sub <- gene_annotation_sample[,c(1:3, 8)]
  names(gene_annotation_sub)[4] <- "gene"
  input_cds <- annotate_cds_by_site(input_cds, gene_annotation_sub)
  num_genes <- pData(input_cds)$num_genes_expressed
  names(num_genes) <- row.names(pData(input_cds))
  unnorm_ga <- build_gene_activity_matrix(input_cds, cons)
  cicero_gene_activities <- normalize_gene_activities(unnorm_ga, num_genes)

cole-trapnell-lab/cicero documentation built on March 13, 2023, 6:02 p.m.