Get negative control genes from each batch of the data
findNCGs(spe, n_assay = 2, batch_name = "SlideName", top_n = 200)A Spatial Experiment object.
Integer to indicate the nth count table in the assay(spe) to be used.
Column name indicating batches.
Integer indicate how many genes to be included as negative control genes.
A Spatial Experiment object, conatining negative control genes in the metadata.
data("dkd_spe_subset")
spe <- findNCGs(dkd_spe_subset, top_n = 100)
#> New names:
#> • `cv` -> `cv...1`
#> • `cv` -> `cv...2`
#> • `cv` -> `cv...3`
#> • `cv` -> `cv...4`
#> • `cv` -> `cv...5`
#> • `cv` -> `cv...6`
#> • `cv` -> `cv...7`
S4Vectors::metadata(spe)$NCGs
#> [1] "CHTF8" "MED13" "PNRC2" "SRSF2" "NFAT5" "RPS26"
#> [7] "HMGN1" "SRRM1" "SIGMAR1" "ZBTB10" "RNASEH2C" "ADIPOR2"
#> [13] "SEC31A" "POLI" "KIR3DL1" "CDC37" "SRP68" "PRPF6"
#> [19] "DAZAP1" "NELFCD" "PNN" "PPP2R2A" "SEC24A" "C1orf50"
#> [25] "RING1" "ZNF444" "SEC61B" "SDAD1" "SF3B3" "ASXL2"
#> [31] "MYO5B" "SNF8" "TBC1D3C" "HARS1" "RRN3" "PURB"
#> [37] "STK25" "PPIAL4F" "KDM6A" "FAM160A2" "DLAT" "ADD3"
#> [43] "C1orf174" "B4GALT3" "FAM204A" "STX12" "UBE2G1" "COQ10B"
#> [49] "ZNF146" "ANP32A" "ATP10A" "ATP8B4" "C9orf16" "COX6B1"
#> [55] "COX7A1" "CPEB1" "FUZ" "ITIH5" "JUNB" "MZT2B"
#> [61] "SLC27A3" "URM1" "PBX4" "KIAA2013" "UPK3B" "MAVS"
#> [67] "EVPL" "DOCK1" "ZNF747" "PHF3" "ARF5" "LIPT2"
#> [73] "VHL" "RAN" "KIAA2026" "FAM111A" "LAMTOR1" "PLEKHM1"
#> [79] "EEF1AKMT2" "PSMB6" "CYB5B" "ASCC3" "MTMR12" "ZMIZ2"
#> [85] "ZNF672" "C12orf65" "TMEM9" "UBXN4" "ZFYVE16" "SLC38A10"
#> [91] "NRSN2" "RABEP2" "CLIC1" "NOMO3" "APH1A" "PPP3CB"
#> [97] "PYGM" "PHIP" "TMEM184B" "ERLEC1"