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

Description Usage Arguments Value Examples

View source: R/fix_bad_mgi_symbols.r

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

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fix_bad_mgi_symbols(exp, mrk_file_path = NULL, printAllBadSymbols = FALSE)

Arguments

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

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

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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)

NathanSkene/EWCE documentation built on June 19, 2021, 5:40 a.m.