Convert candidate genes list into matrix
Usage
matrixize_markers(
marker_df,
ranked = FALSE,
n = NULL,
step_weight = 1,
background_weight = 0,
unique = FALSE,
metadata = NULL,
cluster_col = "classified",
remove_rp = FALSE
)Arguments
- marker_df
dataframe of candidate genes, must contain "gene" and "cluster" columns, or a matrix of gene names to convert to ranked
- ranked
unranked gene list feeds into hyperp, the ranked gene list feeds into regular corr_coef
- n
number of genes to use
- step_weight
ranked genes are tranformed into pseudo expression by descending weight
- background_weight
ranked genes are tranformed into pseudo expression with added weight
- unique
whether to use only unique markers to 1 cluster
- metadata
vector or dataframe of cluster names, should have column named cluster
- cluster_col
column for cluster names to replace original cluster, if metadata is dataframe
- remove_rp
do not include rps, rpl, rp1-9 in markers
Examples
matrixize_markers(pbmc_markers)
#> 0 1 2 3 4 5 6
#> 1 RPS12 IL32 S100A9 CD79A CCL5 CDKN1C GZMB
#> 2 RPS27 LTB S100A8 MS4A1 NKG7 HES4 FGFBP2
#> 3 RPS6 CD3D LGALS2 CD79B GZMA RP11-290F20.3 SPON2
#> 4 RPL32 IL7R FCN1 LINC00926 CST7 MS4A7 PRF1
#> 5 RPS14 LDHB CD14 TCL1A GZMK FCGR3A GNLY
#> 6 RPS25 CD2 TYROBP HLA-DQA1 CTSW CKB AKR1C3
#> 7 RPL9 AQP3 MS4A6A VPREB3 CD8A LILRA3 XCL2
#> 8 RPL13 CD3E CST3 HLA-DQB1 KLRG1 IFITM3 CLIC3
#> 9 RPL31 TPT1 LYZ CD74 GZMH MS4A4A CST7
#> 10 RPS3 TRAT1 TYMP HLA-DRA B2M PILRA KLRD1
#> 11 RPL3 RPS12 CFD FCER2 LYAR LRRC25 GZMA
#> 12 RPL21 SPOCK2 LST1 HLA-DPB1 IL32 LILRB1 NKG7
#> 13 RPS3A CD40LG LGALS1 BANK1 HLA-C RHOC CCL4
#> 14 RPL30 GIMAP7 AIF1 HLA-DRB1 PRF1 SIGLEC10 TTC38
#> 15 LDHB TRADD GSTP1 HLA-DPA1 GZMM HMOX1 PRSS23
#> 16 RPS15A RPS25 GRN TSPAN13 HLA-A LST1 XCL1
#> 17 RPLP2 RPSA GPX1 HLA-DQA2 CD3D CTSL CTSW
#> 18 RPS27A PRDX2 FTL FCRLA PTPRCAP HCK SH2D1B
#> 19 MALAT1 TTC39C S100A6 CD37 CCL4 CSF1R FCGR3A
#> 20 EEF1A1 RPLP0 FTH1 HLA-DRB5 HOPX SERPINA1 IGFBP7
#> 21 RPS13 CD27 FCER1G HVCN1 CD8B FCER1G GZMH
#> 22 RPL13A AES CTSS PKIG MATK CD68 IL2RB
#> 23 RPL27A JUN CD68 HLA-DOB HCST AIF1 KLRF1
#> 24 RPS18 TMEM66 CEBPD BLK SAMD3 CFD S1PR5
#> 25 RPL11 MYL12A S100A4 HLA-DMA HLA-B IFI30 CD247
#> 26 RPS29 RPS29 LGALS3 PDLIM1 NCR3 SPI1 APMAP
#> 27 RPS28 JUNB AP1S2 GNG7 APOBEC3G LILRB2 HOPX
#> 28 RPL35A ANXA1 NPC2 CD72 FGFBP2 BATF3 GPR56
#> 29 RPL23A ARHGAP15 OAZ1 HLA-DMB LCK LILRA5 MATK
#> 30 RPS23 HINT1 CDA P2RX5 MALAT1 STXBP2 GZMM
#> 31 CCR7 EVL S100A11 CD40 C12orf75 WARS C1orf21
#> 32 TPT1 LCK PSAP EAF2 CD99 CXCL16 PLEKHF1
#> 33 RPS20 LAT SAT1 PPAPDC1B GZMB TPPP3 HLA-C
#> 34 CD3D NOSIP NCF2 IRF8 MYL12A C5AR1 B2M
#> 35 RPS4X CD3G CFP RPL18A RARRES3 COTL1 TBX21
#> 36 RPL5 VIM CSF3R CYB561A3 CD2 CEBPB PTGDR
#> 37 RPS16 ITM2A BLVRB QRSL1 DUSP2 MAFB CD7
#> 38 RPL19 OPTN COTL1 MARCH1 CD3E TESC HAVCR2
#> 39 RPL10A MAL SERPINA1 MEF2C CHST12 SLC31A2 TPST2
#> 40 RPSA PLP2 ASGR1 RPS23 HLA-E TIMP1 HLA-A
#> 41 RPS5 FLT3LG NUP214 SMIM14 APMAP IFITM2 PLAC8
#> 42 RPS10 SIT1 GABARAP RPS11 SLC9A3R1 BID FCRL6
#> 43 RPL14 TNFAIP8 ALDH2 RPS5 CD247 ABI3 HLA-B
#> 44 RPS15 RGCC FCGRT LY86 ZAP70 C19orf38 ITGB2
#> 45 RPL18 GSTK1 IFI30 PLEKHF2 LITAF SAT1 CTSC
#> 46 NPM1 FXYD5 CYBA SNX2 MYL12B BRI3 CD63
#> 47 RPLP0 CALM1 FPR1 LTB TPST2 FTH1 NCR3
#> 48 RPL36 PPP2R5C FOLR3 ISG20 MT-CYB CAMK1 ID2
#> 49 CD3E ZFP36L2 PYCARD NCF1 PFN1 PSAP UBB
#> 50 RPL4 ALOX5AP TKT CXCR4 UBC CTD-2006K23.1 C12orf75
#> 51 NOSIP CORO1B SPI1 RPL13A CTSC CTSS SRGN
#> 52 LEF1 SUSD3 RAC1 SNHG7 DDX5 LYN RHOC
#> 53 RPL36A PBXIP1 TSPO LAPTM5 GNLY S100A11 RARRES3
#> 54 EEF1B2 GIMAP5 SLC7A7 RPS8 FYN CFP ARPC5L
#> 55 RPL22 IFITM1 RBP7 RPL15 ANXA1 CST3 PFN1
#> 56 RPL7 IL2RG BRI3 RPL8 ARPC5L TYMP SAMD3
#> 57 RPS8 HSPA8 S100A12 FAIM3 YWHAQ TCF7L2 CCL5
#> 58 PRKCQ-AS1 YWHAQ TNFSF13B RPL18 ID2 FTL APOBEC3G
#> 59 RPL17 RPSAP58 IGSF6 RPS27 CALM1 PTP4A3 CD99
#> 60 PIK3IP1 TNFAIP3 IFITM3 RPL10A IL2RG TYROBP RAP1B
#> 61 JUNB CD69 RNF130 PTPRCAP MYO1F FAM110A CX3CR1
#> 62 TMEM66 GIMAP4 GAPDH STX7 SEPT7 FGL2 FCER1G
#> 63 GLTSCR2 CRIP1 TALDO1 CD52 C9orf142 APOBEC3A PTPRCAP
#> 64 RPS26 ARL6IP5 VCAN GNB2L1 LAT FGR CHST12
#> 65 BTG1 MZT2A BST1 SYPL1 CD53 NPC2 EFHD2
#> 66 CD7 LIMS1 MNDA RPSA SUN2 FAM26F MYL12A
#> 67 RPL38 LEF1 PLBD1 LIMD2 PLEK OAZ1 HLA-E
#> 68 RPL35 FYB APOBEC3A BIRC3 BIN2 CD300LF HCST
#> 69 RPL24 SEPT1 CTSB RPS21 HLA-F SLC7A7 PLEK
#> 70 RPS21 TXN CTSH PRKCB RAP1B CPPED1 ZAP70
#> 71 IL7R PEBP1 IFI6 SNX3 CD3G UNC119 CD300A
#> 72 MAL OCIAD2 NEAT1 EEF2 ANXA6 S100A4 CLIC1
#> 73 RPL37 PIK3IP1 CPVL FAM26F HSP90AA1 NINJ1 ASCL2
#> 74 TCF7 TSTD1 ODF3B POLD4 PIM1 CDA IFITM1
#> 75 C6orf48 SOD1 AP2S1 PLAC8 TUBA4A FCGR2A PDIA3
#> 76 CD27 ILF3-AS1 TGFBI EEF1B2 MT-ND2 HSBP1 ABHD17A
#> 77 RPL34 TCF7 SMCO4 RPL22L1 PTPRC AP2A1 ALOX5AP
#> 78 RPS4Y1 SOCS3 LILRA5 RCSD1 ARL4C PLAUR CCL3
#> 79 RPSAP58 ANKRD12 TMEM176B SEC62 PPP1R18 LGALS1 AOAH
#> 80 LEPROTL1 DNAJB1 SH3BGRL3 PNISR DHRS7 TNFRSF1B IFITM2
#> 81 AES HNRNPF HLA-DRA BLOC1S2 IFITM1 CUX1 C5orf56
#> 82 SELL KLF6 CD33 HMGN1 HSP90B1 EMR2 BST2
#> 83 TMEM123 PPA1 RAB32 TMEM243 STK17A FAM49A CFL1
#> 84 CD3G LEPROTL1 ARPC1B RNASEH2B HSPA5 ACTB PPP1R18
#> 85 RGCC PDCD5 C1orf162 POU2F2 PPP2R5C ARPC3 RAC2
#> 86 GIMAP5 SKP1 TMSB10 CD69 PDIA3 GPBAR1 XBP1
#> 87 LCK RWDD1 ANXA2 DRAM2 UBB LYST ABI3
#> 88 NDFIP1 SLC2A3 STX11 SELL GUK1 MAPKAPK3 TYROBP
#> 89 C12orf57 PSMC5 IL8 EIF4A2 PPIB SLC11A1 MYO1F
#> 90 TOMM7 NSMCE1 CAPG TSC22D3 HNRNPK ADA ARL4C
#> 91 FLT3LG DDIT4 RGS2 ZFP36L1 XBP1 NAAA CD53
#> 92 RHOH TRAM1 PLAUR ATP6V1G1 CCND3 TMSB4X CALM1
#> 93 DNAJB1 EWSR1 CEBPB SP100 RPA2 CASP1 UBE2F
#> 94 GYPC FUS VIM CD53 PPIA PYCARD LITAF
#> 95 TRAT1 NSA2 SRGN DCK RASSF5 YBX1 DHRS7
#> 7 8
#> 1 FCER1A GP9
#> 2 SERPINF1 ITGA2B
#> 3 CLEC10A TMEM40
#> 4 ENHO AP001189.4
#> 5 CLIC2 LY6G6F
#> 6 CD1C SEPT5
#> 7 HLA-DQB2 PTCRA
#> 8 CACNA2D3 TREML1
#> 9 UPK3A CLDN5
#> 10 PHACTR1 HGD
#> 11 HLA-DQA2 RP11-879F14.2
#> 12 BASP1 C2orf88
#> 13 PLD4 SPARC
#> 14 LGMN PF4
#> 15 NDRG2 CMTM5
#> 16 CPVL GNG11
#> 17 CCDC88A GP1BA
#> 18 HLA-DQA1 ITGB3
#> 19 CD33 SDPR
#> 20 GSN SCGB1C1
#> 21 RPS6KA4 CLEC1B
#> 22 SULF2 AC147651.3
#> 23 HLA-DOA PVALB
#> 24 CD1D SCN1B
#> 25 RNASE6 ARHGAP6
#> 26 LMO2 ACRBP
#> 27 HLA-DQB1 FAXDC2
#> 28 HLA-DRB5 MYL9
#> 29 PPP1R14A CLU
#> 30 CSF2RA C19orf33
#> 31 HLA-DMA PDZK1IP1
#> 32 SEMA4A TUBA8
#> 33 HLA-DRB1 CTTN
#> 34 ALDH2 PPBP
#> 35 CD302 ESAM
#> 36 HLA-DPA1 RP11-367G6.3
#> 37 CST3 NRGN
#> 38 HLA-DPB1 TUBB1
#> 39 GNA15 F13A1
#> 40 SPATS2L FSTL1
#> 41 SYK RGS18
#> 42 IL1B ALOX12
#> 43 KLF4 CA2
#> 44 HLA-DMB PTGS1
#> 45 YIF1B CD9
#> 46 HLA-DRA C6orf25
#> 47 ZNF385A HIST1H2AC
#> 48 LILRB4 SNCA
#> 49 GRN GAS2L1
#> 50 CD74 HIST1H2BJ
#> 51 TRIM33 MMD
#> 52 C12orf45 PCP2
#> 53 HAVCR2 TSC22D1
#> 54 CCDC50 DMTN
#> 55 IGSF6 ANKRD9
#> 56 LAP3 ABCC3
#> 57 BLNK RUFY1
#> 58 CTSH PGRMC1
#> 59 CAPG TPM1
#> 60 RNF130 MAP3K7CL
#> 61 ARF3 SENCR
#> 62 ID1 MPP1
#> 63 AP1S2 NGFRAP1
#> 64 SPINT2 TPTEP1
#> 65 RGS1 PDLIM1
#> 66 FAM105A NEXN
#> 67 VCL MLH3
#> 68 LGALS2 TPM4
#> 69 TNFAIP2 ACTN1
#> 70 TPM4 SCFD2
#> 71 MGST2 ILK
#> 72 H2AFY FAM63A
#> 73 LY86 SNN
#> 74 FABP5 PARVB
#> 75 UBL7 GRAP2
#> 76 DDAH2 TMEM91
#> 77 TGFBI MARCH2
#> 78 IFI30 HIST1H2BD
#> 79 GPX1 FAH
#> 80 FDFT1 PLA2G12A
#> 81 FUOM PNMA1
#> 82 IGFLR1 ODC1
#> 83 LSP1 P2RX1
#> 84 MNDA GSN
#> 85 PTPRE NCOA4
#> 86 FCGRT DAAM1
#> 87 GSTP1 CTSA
#> 88 SPI1 FERMT3
#> 89 TAF10 H1F0
#> 90 RAB22A TUBA1C
#> 91 NME1-NME2 KIAA0513
#> 92 LYZ MGLL
#> 93 CFP CALM3
#> 94 SCAMP4 UBL4A
#> 95 CD86 CAPN1