View source: R/fix_bad_mgi_symbols.r
fix_bad_mgi_symbols | 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,
as_sparse = TRUE,
verbose = TRUE,
localHub = FALSE
)
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 |
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. |
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.
# 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)
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