predict_celltypes: Predict cell types

In neurogenomics/MultiEWCE: Multi-Scale Target Explorer

Predict cell types

Description

Predict the causal cell types underlying a patient's phenotypes given some varying degree of prior knowledge.

Usage

predict_celltypes(
  phenotypes,
  diseases_include = NULL,
  diseases_exclude = NULL,
  genes_include = NULL,
  genes_exclude = NULL,
  gene_weights = list(include = 2, default = 1, exclude = 0),
  results = MSTExplorer::load_example_results(),
  phenotype_to_genes = HPOExplorer::load_phenotype_to_genes(),
  agg_var = c("cl_name"),
  effect_var = "logFC",
  x_var = agg_var[1],
  y_var = "score_mean",
  fill_var = "score_sum",
  evidence_score_var = "evidence_score_sum",
  max_x_var = 10,
  subtitle_size = 9,
  plot.margin = ggplot2::margin(1, 1, 1, 40),
  show_plot = TRUE,
  save_path = NULL,
  width = NULL,
  height = NULL
)

Arguments

phenotypes	Phenotypes observed in the patient. Can be a list of HPO phenotype IDs or HPO phenotype names.
diseases_include	Diseases that the patient is known to have. Can be provided as OMIM, Orphanet, or DECIPHER disease IDs.
diseases_exclude	Diseases that the patient is known NOT to have. Can be provided as OMIM, Orphanet, or DECIPHER disease IDs.
genes_include	Genes in which the patient is known to have abnormalities.
genes_exclude	Genes in which the patient is known NOT to have abnormalities.
gene_weights	A named list describing the weight to apply to genes in the include, default, and exclude lists.
results	The cell type-phenotype enrichment results generated by gen_results and merged together with merge_results
phenotype_to_genes	Phenotype to gene mapping from load_phenotype_to_genes.
agg_var	The variable(s) to aggregate results by.
effect_var	Name of the effect size column in the results.
x_var	Variable to plot on the x-axis.
y_var	Variable to plot on the y-axis.
fill_var	Variable to fill by.
evidence_score_var	Which variable from add_evidence to use when weighting genes.
max_x_var	The maximum number of cell types to display.
subtitle_size	Size of the plot subtitle.
plot.margin	margin around entire plot (unit with the sizes of the top, right, bottom, and left margins)
show_plot	Print the plot to the console.
save_path	Save the plot to a file. Set to NULL to not save the plot.
width	Width of the saved plot.
height	Height of the saved plot.

Value

data.table of prioritised cell types, sorted by a "score" that combines:

• The phenotype-cell type enrichment p-values ("p").

• The phenotype-cell type enrichment effect size ("effect").

• A gene-wise factor that upweights/downweights included/excluded genes respectively, multiplied by the evidence score of a phenotype-gene association. Only applied when genes_include or genes_exclude is provided.

Examples

phenotypes <- c("Generalized neonatal hypotonia",
                "Scrotal hypospadias",
                "Increased circulating progesterone")
# diseases_include <- "OMIM:176270"
genes_include <- c("MAGEL2","HERC2")
genes_exclude <- c("SNORD115-1")
ct <- predict_celltypes(phenotypes = phenotypes,
                        genes_include = genes_include,
                        genes_exclude = genes_exclude)

neurogenomics/MultiEWCE documentation built on Sept. 28, 2024, 2:27 a.m.