prepare_quantile_groups: Prepare quantile groups for each celltype based on...

In NathanSkene/MAGMA_Celltyping: Find Causal Cell-Types Underlying Complex Trait Genetics

Prepare quantile groups for each celltype based on specificity

Description

Quantile groups are stored in an extra matrix ('quantiles') in the returned CTD. This function also removes any genes from the CTD data which are not 1:1 orthologs with the GWAS species.

Usage

prepare_quantile_groups(
  ctd,
  standardise = TRUE,
  non121_strategy = "drop_both_species",
  input_species = "mouse",
  output_species = "human",
  numberOfBins = 40,
  verbose = TRUE,
  ...
)

Arguments

ctd	Input CellTypeData.
standardise	Whether to run standardise_ctd first. Provides gene ortholog conversion.
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.
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.
numberOfBins	Number of non-zero quantile bins.
verbose	Print messages. Set verbose=2 if you want to print all messages from internal functions as well.
...	Additional arguments passed to standardise_ctd.

Value

The ctd converted to output_species gene symbols with additional quantiles matrix.

Examples

ctd_orig <- ewceData::ctd()
ctd <- MAGMA.Celltyping::prepare_quantile_groups(ctd = ctd_orig)

NathanSkene/MAGMA_Celltyping documentation built on Aug. 21, 2023, 8:55 a.m.