fix_bad_mgi_symbols {EWCE} | R Documentation |
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)
exp |
An expression matrix where the rows are MGI symbols or an 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 |
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.
library(ewceData) # Load the single cell data cortex_mrna <- 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)