Selects the top N marker genes per cluster from a ranked differential expression result table.
Arguments
- deg
Data frame or matrix. Ranked marker statistics.
- cluster
Character. Column name containing cluster identifiers. Default is `"cluster"`.
- gene
Character. Column name containing gene identifiers. Default is `"gene"`.
- avg_log2FC
Character. Column name for average log2 fold change. Default is `"avg_log2FC"`.
- n
Integer. Number of top markers per cluster. Default is 100.
Examples
deg <- load_data("deg")
get_sig_sc(deg, cluster = "cluster", gene = "gene", avg_log2FC = "avg_log2FC", n = 100)
#> $`Epithelial cells 11`
#> [1] "AQP4" "BCAT1" "RGS16" "LRRN4" "TIMP3"
#> [6] "SUSD2" "AQP1" "CYP4B1" "AGER" "FAM46B"
#> [11] "SCGB3A1" "PEG10" "AK1" "DLX3" "GSTM3"
#> [16] "BTG2" "GDF15" "CTSE" "CLDN18" "EFNA1"
#> [21] "DEGS2" "CYR61" "CKB" "KLHL35" "ARL4D"
#> [26] "C4BPA" "SRRM2" "HMGN2" "SFTPB" "RNASE1"
#> [31] "EGR1" "C16orf89" "IFIT1" "FBLN5" "SFTA2"
#> [36] "IRX5" "GGH" "FABP3" "SULT1A2" "SLC34A2"
#> [41] "CDKN2A" "HMGN3" "RSRP1" "C12orf65" "SFTPD"
#> [46] "ARHGAP24" "TMEM37" "NAPSA" "IGFBP2" "TUBA4A"
#> [51] "CA2" "PIFO" "MLF1" "THUMPD3-AS1" "CLU"
#> [56] "TRA2A" "IFI27" "ATHL1" "ARHGEF2" "CYP51A1"
#> [61] "STMN1" "PGC" "SFPQ" "CDKN1C" "ACBD3"
#> [66] "DGKD" "C19orf53" "FAM177A1" "HIST1H2AM" "SCGB3A2"
#> [71] "ZNF593" "ARHGEF17" "ATP13A4-AS1" "ISG15" "MMP15"
#> [76] "GADD45GIP1" "PEBP4" "ZFAND2A" "PARP1" "TPPP3"
#> [81] "GADD45G" "CD55" "SERTAD1" "RDH10" "OSR2"
#> [86] "CLIC3" "TPPP" "SNRNP25" "C4BPB" "RANBP10"
#> [91] "TNNC1" "CRYM" "PHLDA2" "TFAP2C" "EPHX1"
#> [96] "SFN" "MRPL2" "ZNF493" "SNX22" "ALKBH4"
#>
#> $`Epithelial cells 15`
#> [1] "SFTPC" "SFTPA1" "SFTPA2" "FABP5" "SFTPD"
#> [6] "SFTPB" "PEBP4" "ABCA3" "CSF3R" "NAPSA"
#> [11] "PGC" "WIF1" "MACROD2" "CLDN18" "SLPI"
#> [16] "HP" "DUOX1" "C16orf89" "AQP1" "AK1"
#> [21] "SCGB3A1" "CA2" "SCGB3A2" "SCD" "AFF3"
#> [26] "NECAB1" "FGG" "SLC34A2" "MFSD2A" "GADD45G"
#> [31] "SFTA2" "PTPN13" "RASGRF1" "AQP4" "C1R"
#> [36] "ACOXL" "NR0B2" "PLA2G4F" "DCXR" "SUSD2"
#> [41] "ADIRF" "FILIP1" "RGS16" "MYLK" "HLA-DQB2"
#> [46] "ORM1" "ETV5" "TSPAN7" "CXCL17" "PHYHD1"
#> [51] "RNASE1" "TTN" "SNX30" "C4BPA" "CHI3L1"
#> [56] "IFITM1" "FAM46C" "SFTA1P" "CHI3L2" "GUCY1A3"
#> [61] "CLIC3" "GOLIM4" "EGR1" "TPPP3" "SULT1A2"
#> [66] "CYP4B1" "ATP13A4-AS1" "KCNJ2" "SLC5A2" "TMEM37"
#> [71] "PLLP" "PTTG1" "ARL4D" "PLIN5" "HMGN2"
#> [76] "PMM1" "RSRP1" "CLU" "PIGR" "QDPR"
#> [81] "AGER" "DMBT1" "PEG10" "RSBN1" "CKB"
#> [86] "RMDN2" "CYR61" "NUDT14" "F3" "CTSE"
#> [91] "C3" "TUBA4A" "IRX5" "C12orf65" "CCND3"
#> [96] "TMEM116" "TUBA1B" "PLEKHB1" "IVD" "ACP5"
#>
#> $`Epithelial cells 2`
#> [1] "IGFBP3" "PCDH7" "PTPRN2" "ADAM28" "CASP1" "TRAF2"
#> [7] "CYBA" "SERPINE1" "IL32" "RFK" "TRIM16" "FXYD5"
#> [13] "RAMP1" "EGFL7" "SNAP23" "ATP6V1E1" "HSD11B2" "BATF"
#> [19] "UACA" "TCTN3" "HSPA9" "BIK" "ACSL1" "POLR3K"
#> [25] "CCL28" "AUH" "CMC4" "PRPS1" "EFHD2" "RAB24"
#> [31] "RER1" "HN1" "MTCH2" "NTMT1" "COMTD1" "KRT16"
#> [37] "STX7" "PDCD6IP" "UBTD2" "CHMP1B" "DSC2" "UBA7"
#> [43] "VTA1" "P4HA1" "UFM1" "PTP4A1" "CEBPG" "AMZ2"
#> [49] "PLIN2" "PRPS2" "RNASEH1" "KATNBL1" "PSMD5" "MECR"
#> [55] "DCUN1D1" "PEX19" "TIMM17A" "SGMS1" "C7orf73" "ORC5"
#> [61] "UBQLN1" "VAPA" "PAFAH1B3" "PEX11B" "DRG1" "ADSL"
#> [67] "UBN1" "CLNS1A" "SUMF1" "NSMCE1" "COG7" "DGAT1"
#> [73] "NDUFS3" "YIPF5" "CCDC78" "RAB6A" "LPP" "CHMP2B"
#> [79] "G3BP1" "AAAS" "MOV10" "C3" "CRIP1" "LSG1"
#> [85] "RSPH3" "SNRPA1" "DNAJA3" "HIGD1A" "ARHGDIB" "PIGG"
#> [91] "CCT4" "TES" "CCNJL" "LEPROT" "ATP6V1D" "AFMID"
#> [97] "TALDO1" "NGRN" "PSG5" "CD55"
#>
#> $`Epithelial cells 23`
#> [1] "NECAB1" "SFTPC" "SFTPA1" "PGC" "SFTPA2"
#> [6] "CA2" "PEBP4" "ABCA3" "ETV5" "HNRNPH1"
#> [11] "CHI3L2" "SAR1A" "MFSD2A" "C4BPA" "C1R"
#> [16] "LTF" "F3" "CXCL2" "NR0B2" "PIGR"
#> [21] "FABP5" "SFTPD" "NAPSA" "EGR1" "PTPN13"
#> [26] "SFTPB" "CLU" "RRAD" "WIF1" "DUOX1"
#> [31] "AQP1" "NFKBIZ" "TOB1" "SLC34A2" "TRA2A"
#> [36] "RASGRF1" "UGCG" "HACD1" "PHYHD1" "AFF3"
#> [41] "CHI3L1" "GOLIM4" "CD274" "KCNJ2" "SLC38A2"
#> [46] "PPP3CA" "C16orf89" "ACOXL" "SCD" "SKIL"
#> [51] "RDH10" "WTAP" "TSC22D2" "SCGB3A1" "ARGLU1"
#> [56] "DMBT1" "AZGP1" "C8orf4" "NNMT" "RNASE1"
#> [61] "PLA2G4F" "NUCKS1" "FGG" "LRRC75A-AS1" "UBE2B"
#> [66] "SERTAD1" "HMGCS1" "MBNL1" "PLIN5" "ADAM17"
#> [71] "DDX3X" "CTNNB1" "FAM46B" "PPP1CB" "CLDN18"
#> [76] "ATP13A4-AS1" "SNX30" "CYP51A1" "PTP4A1" "SUSD2"
#> [81] "TFAP2C" "HP" "STOM" "STAM" "RAB21"
#> [86] "MPZL3" "CRIM1" "MACROD2" "STK17A" "UGDH"
#> [91] "KCTD9" "ALDH6A1" "FNIP1" "ZC3H4" "DUSP14"
#> [96] "CXCL17" "DCBLD2" "PPP6R3" "ARL8B" "SLMO2"
#>
#> $`Epithelial cells 25`
#> [1] "LYPD2" "REG1A" "SERPINB3" "SERPINB5" "CLDN10"
#> [6] "ARL14" "SERPINB4" "MUC5AC" "AKR1C2" "KRT17"
#> [11] "IL1RN" "ALDH3A1" "C12orf75" "SERPINA3" "KRT6A"
#> [16] "BASP1" "BPIFB1" "PRKCDBP" "CDKN2A" "HNRNPH1"
#> [21] "SFN" "MUC5B" "CXCL1" "RARRES1" "F3"
#> [26] "IFITM1" "NUCKS1" "MLF1" "ST6GAL1" "EREG"
#> [31] "OXCT1" "MAFIP" "IFI27" "KLK11" "PHLDA2"
#> [36] "TIMP1" "TOB1" "LRRC75A-AS1" "S100A2" "EEF1B2"
#> [41] "PADI2" "AEN" "BCL10" "EGR1" "HMGCS1"
#> [46] "WTAP" "TRA2A" "HACD1" "BTG2" "AKR1C1"
#> [51] "SKIL" "OLFM1" "MPRIP" "SNRPB" "WEE1"
#> [56] "JAG1" "SLC7A5P2" "ATHL1" "EFHD2" "GMDS"
#> [61] "C12orf57" "IL17RB" "GGH" "UGCG" "MIR205HG"
#> [66] "STAT2" "SERTAD1" "R3HDM2" "CTNNB1" "NCOR1"
#> [71] "ARGLU1" "PDCD4" "CLTB" "GMNN" "RIN2"
#> [76] "PPP3CA" "UBE2B" "SLC5A2" "PPP1CB" "STON2"
#> [81] "DST" "KIAA1217" "ARFIP2" "FAM208B" "RASSF6"
#> [86] "HIST1H2AM" "SMURF2" "FKBP9" "ARL8B" "RREB1"
#> [91] "UGDH" "HIST1H4C" "HMGN3" "BIK" "B3GALNT2"
#> [96] "C4BPB" "TRIM16" "PDGFA" "ZC3H4" "HMGCR"
#>
#> $`Epithelial cells 26`
#> [1] "ITLN2" "FMO2" "RTKN2" "AGER" "HEG1" "CRYAB"
#> [7] "IGFBP7" "CLDN18" "SPOCK2" "UPK3B" "CYP4B1" "TNNC1"
#> [13] "PDPN" "ADIRF" "SFTA1P" "TIMP3" "KLK11" "COL4A2"
#> [19] "AQP4" "ABCA1" "PLLP" "CLIC3" "RGCC" "CCND2"
#> [25] "TAGLN" "SUSD2" "SBSPON" "RNASE1" "WFS1" "MGLL"
#> [31] "MAP2" "SULT1A2" "TUBA1A" "UNC13D" "IFI27" "CD55"
#> [37] "FKBP1B" "AKR1C1" "RIN2" "F3" "FILIP1" "FN1"
#> [43] "PEBP4" "FAM46B" "SFTA2" "PRKCDBP" "CRIP1" "TMEM98"
#> [49] "CEACAM6" "CKB" "FBLN5" "PHACTR2" "EPB41L5" "DST"
#> [55] "ARHGAP24" "PEG10" "ABI3BP" "LRRN4" "TSPAN7" "CTGF"
#> [61] "FBXL15" "STOM" "HMGN2" "SDC1" "STON2" "QKI"
#> [67] "RFC1" "PDGFA" "FAS" "IFT43" "TXNRD2" "DUOX1"
#> [73] "ARL8B" "NHLRC3" "TERF1" "SNX22" "CYR61" "RBM17"
#> [79] "TJP1" "SAP30BP" "SGMS1" "ARAP2" "HSD17B8" "MICA"
#> [85] "STX7" "TRIM5" "VPS4B" "PDS5B" "NUCKS1" "PCMTD1"
#> [91] "SFTPB" "MDM4" "FAM134A" "ACAA2" "CTSE" "ABCA7"
#> [97] "SNRPB" "CIAPIN1" "HNRNPA0" "PHF10"
#>
#> $`Epithelial cells 27`
#> [1] "APOBEC3H" "ALDH3A1" "LDHD"
#> [4] "AZGP1" "SCGB3A2" "MT1G"
#> [7] "KLK11" "TPPP3" "TMEM37"
#> [10] "RASL11A" "CTSE" "CEACAM5"
#> [13] "DEGS2" "ITPR2" "NHS"
#> [16] "LL22NC03-75H12.2" "TMEM98" "C16orf89"
#> [19] "C4BPA" "HLA-DQB2" "SLC1A7"
#> [22] "GSTA1" "AKR7A2" "BTG2"
#> [25] "CXCL17" "RARRES2" "IGFBP2"
#> [28] "TMEM230" "SUSD2" "CYP4B1"
#> [31] "PPIE" "SYT2" "LINC00578"
#> [34] "TERF2IP" "SRRM2" "SFTA2"
#> [37] "PMM1" "DHRS4-AS1" "GDF15"
#> [40] "SFTPB" "NME3" "CXCL14"
#> [43] "PLLP" "CLU" "ELOVL1"
#> [46] "SFTPD" "PEMT" "MLF1"
#> [49] "IFI27" "MRPL57" "NGDN"
#> [52] "SNRPB" "SNRNP25" "MTSS1L"
#> [55] "UBE2I" "MAFIP" "AQP4"
#> [58] "SCGB3A1" "CHMP4A" "PIGR"
#> [61] "ITPA" "IRX5" "CEACAM6"
#> [64] "SZT2" "TMEM205" "RGS16"
#> [67] "DNAJA3" "NAPSA" "TMEM52"
#> [70] "POLR3K" "GFRA3" "MSRB1"
#> [73] "CCDC101" "IVD" "PCNA"
#> [76] "NUDT16L1" "HLA-DOB" "BCL6"
#> [79] "FTO" "SFTA1P" "C10orf32"
#> [82] "MLYCD" "AK1" "CCDC115"
#> [85] "DMBT1" "RNASE1" "CIAPIN1"
#> [88] "FAM71E1" "COQ9" "CPAMD8"
#> [91] "ALDH6A1" "MMP15" "PLEKHB1"
#> [94] "RMDN2" "LYRM1" "HSD17B8"
#> [97] "YRDC" "ERAL1" "SLC5A2"
#> [100] "MMP7"
#>
#> $`Epithelial cells 28`
#> [1] "UPK1B" "BPIFB1" "KLK6" "PSG3" "PPBP"
#> [6] "LDLRAD1" "PADI2" "MSMB" "ADGRE2" "PSG5"
#> [11] "IGFBP3" "SLC30A2" "APOD" "TALDO1" "KRT6A"
#> [16] "KRT16" "TMEM140" "IL3RA" "KRT4" "CHMP1B"
#> [21] "ZNF793-AS1" "TRIM16" "P4HA1" "APOL2" "WFS1"
#> [26] "KRT17" "MARCKS" "KRT13" "MOV10" "HDAC9"
#> [31] "CLN5" "RNF13" "CLP1" "DAZAP2" "WEE1"
#> [36] "BIK" "UACA" "RNF114" "DYNLL1" "S100A9"
#> [41] "NDRG3" "TMEM106C" "QRICH1" "SUMF1" "CSTF1"
#> [46] "PPAP2B" "P4HTM" "LOC283788" "CHID1" "UBE2D1"
#> [51] "ARFIP2" "RARRES1" "UNG" "TBC1D1" "SERPINE1"
#> [56] "PEX11B" "TMTC3" "TOMM34" "NARS" "STOM"
#> [61] "UBQLN1" "PIGG" "COMMD7" "RFK" "BLOC1S4"
#> [66] "ADAM10" "TFAP2C" "CTNNB1" "FUBP1" "HAT1"
#> [71] "CRIP1" "C3" "HNRNPC" "VTA1" "CCT4"
#> [76] "PDCD6IP" "LSG1" "SNAP23" "HIGD1A" "PAFAH1B3"
#> [81] "AAAS" "PIP4K2C" "CLIC3" "RER1" "UBA7"
#> [86] "RSPH3" "UFM1" "AUH" "CEACAM5" "VPS41"
#> [91] "TCTN3" "TJP1" "IFIT2" "CCL28" "CHMP2B"
#> [96] "COG7" "ACTR10" "FXYD5" "PTP4A1" "HSPA9"
#>
#> $`Epithelial cells 29`
#> [1] "PRSS2" "PRSS1" "PRSS3" "ATG9B" "PLA1A"
#> [6] "PAEP" "AZGP1" "UBE2C" "TNFRSF18" "G0S2"
#> [11] "CDA" "ALDOC" "NME1-NME2" "MIR205HG" "CDKN2A"
#> [16] "AKR1B1" "CHI3L1" "C4orf48" "YEATS4" "MAP1B"
#> [21] "TNNC2" "RGS17" "PPAT" "MSRB1" "ZNF593"
#> [26] "LAGE3" "RAN" "ICT1" "NOP16" "RASSF3"
#> [31] "EEF1B2" "SLC27A5" "MYEOV2" "GEMIN6" "TIMP1"
#> [36] "CEACAM5" "CD320" "HN1" "MRPL13" "APOD"
#> [41] "S100A2" "MRPL32" "MRPL21" "PAFAH1B3" "GDF15"
#> [46] "GADD45GIP1" "PHLDA2" "QTRTD1" "ANGPTL4" "C19orf24"
#> [51] "POLE4" "SUPT4H1" "MTIF2" "MRPL57" "DDX18"
#> [56] "ACOX2" "SDC1" "CCDC59" "DST" "ATP5D"
#> [61] "SNHG17" "SLC34A2" "DCBLD2" "SNRNP25" "NIFK"
#> [66] "MPHOSPH10" "NAA10" "TBCB" "S100A9" "PLIN2"
#> [71] "MRPL40" "ITPA" "TFAM" "TMEM61" "TMEM98"
#> [76] "GPATCH4" "TRMT10C" "SLMO2" "RPS19BP1" "RPP21"
#> [81] "NUFIP2" "NAPSA" "RAMP1" "MEA1" "NSMCE1"
#> [86] "CEBPZOS" "APOL2" "TMEM14A" "COMTD1" "PSMD9"
#> [91] "DTYMK" "SNHG11" "HINT2" "NT5C" "TMEM91"
#> [96] "SFTA2" "AP1AR" "POLR3K" "GOLT1A" "SMIM6"
#>
#> $`Epithelial cells 6`
#> [1] "PTN" "CHGB" "NR2F1-AS1" "CRLF1" "PGF"
#> [6] "MUC5B" "MGP" "COL1A1" "CCDC80" "KRT81"
#> [11] "MIR205HG" "CEACAM6" "IFITM1" "NHS" "EREG"
#> [16] "RGS17" "CDKN2A" "CCL2" "CAMK1D" "S100A9"
#> [21] "IFI27" "PHGDH" "SNHG18" "DMBT1" "CEMIP"
#> [26] "NNMT" "ARL4A" "CXCL14" "OXCT1" "CEACAM5"
#> [31] "TNFRSF18" "TGM2" "THBS1" "CYSLTR1" "COL17A1"
#> [36] "HDGFRP3" "LOC648987" "EMB" "TNFSF10" "SPON2"
#> [41] "ARHGDIB" "PIGR" "NR1D1" "CLEC2D" "RN7SK"
#> [46] "RNASE1" "TIMP1" "SLC38A1" "CXCL1" "CDKN1C"
#> [51] "ATHL1" "TGFBI" "MARCKS" "SLC12A2" "GUCY1A3"
#> [56] "PHLDA2" "TRA2A" "EXOC3-AS1" "LRRC37A4P" "C4orf48"
#> [61] "C21orf2" "WEE1" "PIP4K2C" "CD320" "C12orf57"
#> [66] "IGFBP2" "C8orf4" "TMEM205" "XRRA1" "IRF2BPL"
#> [71] "STON2" "RRAD" "SNHG1" "EPHX1" "ISG15"
#> [76] "TMEM238" "MRPL39" "IRF7" "CHI3L1" "NFKBIZ"
#> [81] "CCDC85B" "YBEY" "LINC00649" "C4BPB" "ZNF195"
#> [86] "KRT17" "ATP5D" "PDK3" "CAPS" "PMAIP1"
#> [91] "IVD" "DST" "HSPA6" "SAC3D1" "UBE2S"
#> [96] "ABCA7" "SEPT11" "C19orf60" "HPGD" "GADD45GIP1"
#>