Query genes in specificity matrices. — query_gene

Allows user to query a vector of genes in a celltype_data file with mean expression and specificity matrices.

query_gene_ctd(
  genes,
  ...,
  celltypeLevel = c(1, 2),
  median_included = FALSE,
  genelistSpecies = c("mouse", "human"),
  ctdSpecies = c("mouse", "human")
)

Arguments

genes: Query genes as a vector.
...: Names of input ctds. An individual ctd, should have been generated using generate.celltype.data from the EWCE package, and contains mean expression and specificity matrices from a scRNAseq study.
celltypeLevel: Either 1 or 2, depending on whether user wants to query level 1 or 2 cell types.
median_included: logical. If from newer version of EWCE ctd may include median expression and specificity. Setting to TRUE will include these in the final table.
genelistSpecies: Either 'mouse' or 'human' depending on whether MGI or HGNC symbols are used.
ctdSpecies: Either 'mouse' or 'human' depending on the ctd datasets being used. Species must be the same across all input ctds.

Value

Outputs a dataframe, with mean expression and specificity per gene from each study.