R/fix_bad_mgi_symbols.r
fix_bad_mgi_symbols.Rd
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.
fix_bad_mgi_symbols( exp, mrk_file_path = NULL, printAllBadSymbols = FALSE, as_sparse = TRUE, verbose = TRUE )
exp | An expression matrix where the rows are MGI symbols, or a SingleCellExperiment (SCE) or other Ranged Summarized Experiment (SE) type object. |
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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 |
verbose | Print messages. |
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.
#>#># 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)#>#>#>#>#>#>#>#>#>#>#>