standardise_ctd: Convert a CellTypeDataset into standardized format

In NathanSkene/EWCE: Expression Weighted Celltype Enrichment

Convert a CellTypeDataset into standardized format

Description

This function will take a CTD, drop all genes without 1:1 orthologs with the output_species ("human" by default), convert the remaining genes to gene symbols, assign names to each level, and convert all matrices to sparse matrices and/or DelayedArray.

Usage

standardise_ctd(
  ctd,
  dataset,
  input_species = NULL,
  output_species = "human",
  sctSpecies_origin = input_species,
  non121_strategy = "drop_both_species",
  method = "homologene",
  force_new_quantiles = TRUE,
  force_standardise = FALSE,
  remove_unlabeled_clusters = FALSE,
  numberOfBins = 40,
  keep_annot = TRUE,
  keep_plots = TRUE,
  as_sparse = TRUE,
  as_DelayedArray = FALSE,
  rename_columns = TRUE,
  make_columns_unique = FALSE,
  verbose = TRUE,
  ...
)

Arguments

ctd	Input CellTypeData.
dataset	CellTypeData. name.
input_species	Which species the gene names in exp come from. See list_species for all available species.
output_species	Which species' genes names to convert exp to. See list_species for all available species.
sctSpecies_origin	Species that the sct_data originally came from, regardless of its current gene format (e.g. it was previously converted from mouse to human gene orthologs). This is used for computing an appropriate backgrund.
non121_strategy	How to handle genes that don't have 1:1 mappings between input_species:output_species. Options include: "drop_both_species" or "dbs" or 1 : Drop genes that have duplicate mappings in either the input_species or output_species (DEFAULT). "drop_input_species" or "dis" or 2 : Only drop genes that have duplicate mappings in the input_species. "drop_output_species" or "dos" or 3 : Only drop genes that have duplicate mappings in the output_species. "keep_both_species" or "kbs" or 4 : Keep all genes regardless of whether they have duplicate mappings in either species. "keep_popular" or "kp" or 5 : Return only the most "popular" interspecies ortholog mappings. This procedure tends to yield a greater number of returned genes but at the cost of many of them not being true biological 1:1 orthologs. "sum","mean","median","min" or "max" : When gene_df is a matrix and gene_output="rownames", these options will aggregate many-to-one gene mappings (input_species-to-output_species) after dropping any duplicate genes in the output_species.
method	R package to use for gene mapping: "gprofiler" : Slower but more species and genes. "homologene" : Faster but fewer species and genes. "babelgene" : Faster but fewer species and genes. Also gives consensus scores for each gene mapping based on a several different data sources.
force_new_quantiles	By default, quantile computation is skipped if they have already been computed. Set =TRUE to override this and generate new quantiles.
force_standardise	If ctd has already been standardised, whether to rerun standardisation anyway (Default: FALSE).
remove_unlabeled_clusters	Remove any samples that have numeric column names.
numberOfBins	Number of non-zero quantile bins.
keep_annot	Keep the column annotation data if provided.
keep_plots	Keep the dendrograms if provided.
as_sparse	Convert to sparse matrix.
as_DelayedArray	Convert to DelayedArray.
rename_columns	Remove replace_chars from column names.
make_columns_unique	Rename each columns with the prefix dataset.species.celltype.
verbose	Print messages. Set verbose=2 if you want to print all messages from internal functions as well.
...	Arguments passed on to orthogene::convert_orthologs gene_df Data object containing the genes (see gene_input for options on how the genes can be stored within the object). Can be one of the following formats: matrix : A sparse or dense matrix. data.frame : A data.frame, data.table. or tibble. codelist : A list or character vector. Genes, transcripts, proteins, SNPs, or genomic ranges can be provided in any format (HGNC, Ensembl, RefSeq, UniProt, etc.) and will be automatically converted to gene symbols unless specified otherwise with the ... arguments. Note: If you set method="homologene", you must either supply genes in gene symbol format (e.g. "Sox2") OR set standardise_genes=TRUE. gene_input Which aspect of gene_df to get gene names from: "rownames" : From row names of data.frame/matrix. "colnames" : From column names of data.frame/matrix. <column name> : From a column in gene_df, e.g. "gene_names". gene_output How to return genes. Options include: "rownames" : As row names of gene_df. "colnames" : As column names of gene_df. "columns" : As new columns "input_gene", "ortholog_gene" (and "input_gene_standard" if standardise_genes=TRUE) in gene_df. "dict" : As a dictionary (named list) where the names are input_gene and the values are ortholog_gene. "dict_rev" : As a reversed dictionary (named list) where the names are ortholog_gene and the values are input_gene. standardise_genes If TRUE AND gene_output="columns", a new column "input_gene_standard" will be added to gene_df containing standardised HGNC symbols identified by gorth. drop_nonorths Drop genes that don't have an ortholog in the output_species. agg_fun Aggregation function passed to aggregate_mapped_genes. Set to NULL to skip aggregation step (default). mthreshold Maximum number of ortholog names per gene to show. Passed to gorth. Only used when method="gprofiler" (DEFAULT : Inf). sort_rows Sort gene_df rows alphanumerically. gene_map A data.frame that maps the current gene names to new gene names. This function's behaviour will adapt to different situations as follows: gene_map=<data.frame> : When a data.frame containing the gene key:value columns (specified by input_col and output_col, respectively) is provided, this will be used to perform aggregation/expansion. gene_map=NULL and input_species!=output_species : A gene_map is automatically generated by map_orthologs to perform inter-species gene aggregation/expansion. gene_map=NULL and input_species==output_species : A gene_map is automatically generated by map_genes to perform within-species gene gene symbol standardization and aggregation/expansion. input_col Column name within gene_map with gene names matching the row names of X. output_col Column name within gene_map with gene names that you wish you map the row names of X onto.

Value

Standardised CellTypeDataset.

Examples

ctd <- ewceData::ctd()
ctd_std <- EWCE::standardise_ctd(
    ctd = ctd,
    input_species = "mouse",
    dataset = "Zeisel2016"
)

NathanSkene/EWCE documentation built on April 10, 2024, 1:02 a.m.