fix_bad_mgi_symbols: fix_bad_mgi_symbols - Given an expression matrix, wherein the...

In NathanSkene/EWCE: Expression Weighted Celltype Enrichment

fix_bad_mgi_symbols - Given an expression matrix, wherein the rows are supposed to be MGI symbols, find those symbols which are not official MGI symbols, then check in the MGI synonm database for whether they match to a proper MGI symbol. Where a symbol is found to be an aliases for a gene that is already in the dataset, the combined reads are summed together.

Description

Also checks whether any gene names contain "Sep", "Mar" or "Feb". These should be checked for any suggestion that excel has corrupted the gene names.

Usage

fix_bad_mgi_symbols(
  exp,
  mrk_file_path = NULL,
  printAllBadSymbols = FALSE,
  as_sparse = TRUE,
  verbose = TRUE,
  localHub = FALSE
)

Arguments

exp	An expression matrix where the rows are MGI symbols, or a SingleCellExperiment (SCE) or other Ranged Summarized Experiment (SE) type object.
mrk_file_path	Path to the MRK_List2 file which can be downloaded from www.informatics.jax.org/downloads/reports/index.html
printAllBadSymbols	Output to console all the bad gene symbols
as_sparse	Convert exp to sparse matrix.
verbose	Print messages.
localHub	If working offline, add argument localHub=TRUE to work with a local, non-updated hub; It will only have resources available that have previously been downloaded. If offline, Please also see BiocManager vignette section on offline use to ensure proper functionality.

Value

Returns the expression matrix with the rownames corrected and rows representing the same gene merged. If no corrections are necessary, input expression matrix is returned. If a SingleCellExperiment (SCE) or other Ranged Summarized Experiment (SE) type object was inputted this will be returned with the corrected expression matrix under counts.

Examples

# Load the single cell data
cortex_mrna <- ewceData::cortex_mrna()
# take a subset for speed
cortex_mrna$exp <- cortex_mrna$exp[1:50, 1:5]
cortex_mrna$exp <- fix_bad_mgi_symbols(cortex_mrna$exp)

NathanSkene/EWCE documentation built on Nov. 3, 2024, 8:16 a.m.