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Calculate GeneActivityScores

Source: R/geneScores.R
gene_scores.Rd

Gene activity scores can be calculated as a distance-weighted sum of per-tile accessibility. The tile weights for each gene can be represented as a sparse matrix of dimension genes x tiles. If we multiply this weight matrix by a corresponding tile matrix (tiles x cells), then we can get a gene activity score matrix of genes x cells. gene_score_weights_archr() calculates the weight matrix (best if you have a pre-computed tile matrix), while gene_score_archr() provides a easy-to-use wrapper.

Usage

gene_score_weights_archr(
  genes,
  chromosome_sizes,
  blacklist = NULL,
  tile_width = 500,
  gene_name_column = "gene_id",
  addArchRBug = FALSE
)

gene_score_archr(
  fragments,
  genes,
  chromosome_sizes,
  blacklist = NULL,
  tile_width = 500,
  gene_name_column = "gene_id",
  addArchRBug = FALSE,
  tile_max_count = 4,
  scale_factor = 10000,
  tile_matrix_path = tempfile(pattern = "gene_score_tile_mat")
)

Arguments

genes

Gene coordinates given as GRanges, data.frame, or list. See help("genomic-ranges-like") for details on format and coordinate systems. Required attributes:

  • chr, start, end: genomic position

  • strand: +/- or TRUE/FALSE for positive or negative strand

chromosome_sizes

Chromosome start and end coordinates given as GRanges, data.frame, or list. See help("genomic-ranges-like") for details on format and coordinate systems. Required attributes:

  • chr, start, end: genomic position

See read_ucsc_chrom_sizes().

blacklist

Regions to exclude from calculations, given as GRanges, data.frame, or list. See help("genomic-ranges-like") for details on format and coordinate systems. Required attributes:

  • chr, start, end: genomic position

tile_width

Size of tiles to consider

gene_name_column

If not NULL, a column name of genes to use as row names

addArchRBug

Replicate ArchR bug in handling nested genes

fragments

Input fragments object

tile_max_count

Maximum value in the tile counts matrix. If not null, tile counts higher than this will be clipped to tile_max_count. Equivalent to ceiling argument of ArchR::addGeneScoreMatrix()

scale_factor

If not null, counts for each cell will be scaled to sum to scale_factor. Equivalent to scaleTo argument of ArchR::addGeneScoreMatrix()

tile_matrix_path

Path of a directory where the intermediate tile matrix will be saved

Value

gene_score_weights_archr

Weight matrix of dimension genes x tiles

gene_score_archr

Gene score matrix of dimension genes x cells.

Details

gene_score_weights_archr:

Given a set of tile coordinates and distances returned by gene_score_tiles_archr(), calculate a weight matrix of dimensions genes x tiles. This matrix can be multiplied with a tile matrix to obtain ArchR-compatible gene activity scores.