normalize_gene_activities {cicero} | R Documentation

## 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)

[Package cicero version 1.4.4 Index]