Remove genes show high signal in the background expression data from markers.

remove_bg_exp_mat(sig_mat, bg_mat, markers, snr = 1, gene_id = "SYMBOL")

Arguments

sig_mat: log-transformed expression matrix of interested signal data
bg_mat: log-transformed expression matrix of interested background data
markers: vector, a vector of gene names, listed the gene symbols to be filtered. Must be gene SYMBOLs.
snr: num, the cutoff of SNR to screen markers which are not or lowly expressed in bg_data
gene_id: character, specify the gene ID types of row names of sig_mat and bg_mat data, could be one of 'ENSEMBL', 'SYMBOL', 'ENTREZ'..., default 'SYMBOL'

Value

a vector of genes after filtration

Examples

data("im_data_6", "nk_markers", "ccle_crc_5")
remove_bg_exp_mat(
  sig_mat = Biobase::exprs(im_data_6),
  bg_mat = ccle_crc_5$counts,
  markers = nk_markers$HGNC_Symbol[30:40],
  gene_id = c("ENSEMBL", "SYMBOL")
)
#> 'select()' returned 1:1 mapping between keys and columns
#>  [1] "GRAP2"  "GZMB"   "GNLY"   "FASLG"  "GPR18"  "GZMA"   "GFI1"   "FCGR3B"
#>  [9] "EOMES"  "GPR171" "FCGR3A"