fix_bad_hgnc_symbols: fix_bad_hgnc_symbols

In NathanSkene/EWCE: Expression Weighted Celltype Enrichment

fix_bad_hgnc_symbols

Description

Given an expression matrix, wherein the rows are supposed to be HGNC symbols, find those symbols which are not official HGNC symbols, then correct them if possible. Return the expression matrix with corrected symbols.

Usage

fix_bad_hgnc_symbols(
  exp,
  dropNonHGNC = FALSE,
  as_sparse = TRUE,
  verbose = TRUE,
  localHub = FALSE
)

Arguments

exp	An expression matrix where the rows are HGNC symbols or a SingleCellExperiment (SCE) or other Ranged Summarized Experiment (SE) type object.
dropNonHGNC	Boolean. Should symbols not recognised as HGNC symbols be dropped?
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 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

# create example expression matrix, could be part of a exp, annot list obj
exp <- matrix(data = runif(70), ncol = 10)
# Add HGNC gene names but add with an error:
# MARCH8 is a HGNC symbol which if opened in excel will convert to Mar-08
rownames(exp) <-
    c("MT-TF", "MT-RNR1", "MT-TV", "MT-RNR2", "MT-TL1", "MT-ND1", "Mar-08")
exp <- fix_bad_hgnc_symbols(exp)
# fix_bad_hgnc_symbols warns the user of this possible issue

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