Run differential expression analysis on a Seurat object
Usage
RunSeuratDEAnalysis(
object,
group_by,
ident_1 = NULL,
ident_2 = NULL,
assay = NULL,
subset = NULL,
cache = NULL,
error = TRUE,
...
)Arguments
- object
Seurat object
- group_by
Column name in meta.data to group cells by
- ident_1
Identity of the first group of cells
- ident_2
Identity of the second group of cells
- assay
Assay to use for analysis
- subset
Subset of cells to use for analysis It should be a string of expression to pass to
dplyr::filterfunction- cache
Directory to cache the results. Set to
FALSEto disable caching The results of the analysis will be saved in this directory Anything changed in the object or arguments will trigger a re-run- error
Whether to raise an error if the analysis fails Otherwise, return an empty data frame
- ...
Additional arguments to pass to
Seurat::FindMarkers()
Examples
RunSeuratDEAnalysis(SeuratObject::pbmc_small, "groups", "g1", "g2")
#> Warning: `when()` was deprecated in purrr 1.0.0.
#> ℹ Please use `if` instead.
#> ℹ The deprecated feature was likely used in the tidyseurat package.
#> Please report the issue at
#> <https://github.com/stemangiola/tidyseurat/issues>.
#> p_val avg_log2FC pct.1 pct.2 p_val_adj gene groups
#> NOSIP 0.02870319 1.2224797 0.455 0.194 1 NOSIP g2:g1
#> LYAR 0.02920961 0.8205500 0.159 0.389 1 LYAR g2:g1
#> SNHG7 0.03189563 0.9583741 0.295 0.083 1 SNHG7 g2:g1
#> TMUB1 0.03592718 1.7965894 0.182 0.028 1 TMUB1 g2:g1
#> ZNF330 0.03911949 9.7197369 0.114 0.000 1 ZNF330 g2:g1
#> FUOM 0.03911949 7.6369685 0.114 0.000 1 FUOM g2:g1
#> CCL4 0.04262696 3.6666376 0.205 0.056 1 CCL4 g2:g1
#> LINC00936 0.04918625 0.7604677 0.386 0.167 1 LINC00936 g2:g1
#> TSPO 0.05000053 0.8252648 0.659 0.361 1 TSPO g2:g1
#> IFI6 0.05588343 0.8570195 0.432 0.222 1 IFI6 g2:g1
#> VDAC3 0.06665008 3.6742886 0.318 0.139 1 VDAC3 g2:g1
#> SPON2 0.07526141 1.7237839 0.273 0.111 1 SPON2 g2:g1
#> LGALS2 0.08238383 1.4537375 0.341 0.167 1 LGALS2 g2:g1
#> RPL7L1 0.08259804 -2.5594238 0.091 0.222 1 RPL7L1 g2:g1
#> TAF7 0.08349570 1.5772505 0.341 0.167 1 TAF7 g2:g1
#> FCGR3A 0.08436567 1.1275295 0.432 0.250 1 FCGR3A g2:g1
#> LGALS9 0.08733037 1.1241969 0.273 0.111 1 LGALS9 g2:g1
#> GZMB 0.08733037 1.1698448 0.273 0.111 1 GZMB g2:g1
#> CLEC10A 0.09071524 1.6996524 0.182 0.056 1 CLEC10A g2:g1
#> FCER1A 0.09397257 1.9329064 0.182 0.056 1 FCER1A g2:g1
#> LRRC25 0.09529164 0.4200849 0.273 0.111 1 LRRC25 g2:g1
#> BANK1 0.09545145 2.0219200 0.136 0.028 1 BANK1 g2:g1
#> GSTP1 0.09628003 0.7713358 0.591 0.444 1 GSTP1 g2:g1
#> SIT1 0.09934503 -3.6034439 0.023 0.111 1 SIT1 g2:g1
#> ARHGDIA 0.10084609 -0.4601009 0.432 0.250 1 ARHGDIA g2:g1
#> HLA-DMA 0.10813435 1.0195709 0.386 0.222 1 HLA-DMA g2:g1
#> GRN 0.11667166 0.5547349 0.409 0.222 1 GRN g2:g1
#> RUFY1 0.11768586 -0.9810894 0.091 0.222 1 RUFY1 g2:g1
#> MS4A7 0.12277557 0.5415504 0.227 0.083 1 MS4A7 g2:g1
#> IFI30 0.13211385 0.4138543 0.341 0.167 1 IFI30 g2:g1
#> RGS1 0.13634254 2.5506416 0.159 0.056 1 RGS1 g2:g1
#> THYN1 0.14336601 1.5281674 0.205 0.083 1 THYN1 g2:g1
#> PARVB 0.15081270 -1.4496990 0.068 0.167 1 PARVB g2:g1
#> PCMT1 0.15207496 3.3593272 0.295 0.167 1 PCMT1 g2:g1
#> FCGRT 0.16468927 0.9702779 0.409 0.250 1 FCGRT g2:g1
#> BID 0.17214063 1.1827776 0.386 0.222 1 BID g2:g1
#> GNLY 0.17975936 1.3725474 0.295 0.167 1 GNLY g2:g1
#> FCER1G 0.18735817 0.6490939 0.636 0.472 1 FCER1G g2:g1
#> TAGAP 0.18771440 -0.4875612 0.114 0.222 1 TAGAP g2:g1
#> BLVRA 0.19048552 -1.1214685 0.227 0.333 1 BLVRA g2:g1
#> COTL1 0.19393336 0.4875465 0.750 0.583 1 COTL1 g2:g1
#> HLA-DQA1 0.21368858 0.9605902 0.386 0.250 1 HLA-DQA1 g2:g1
#> VPS28 0.21488446 -1.2334213 0.318 0.444 1 VPS28 g2:g1
#> GIMAP1 0.22134291 0.9678929 0.409 0.250 1 GIMAP1 g2:g1
#> PRF1 0.22555711 0.3097331 0.295 0.167 1 PRF1 g2:g1
#> SAFB2 0.23520876 2.4093824 0.091 0.028 1 SAFB2 g2:g1
#> EIF3G 0.23894997 0.7393618 0.591 0.417 1 EIF3G g2:g1
#> NRBP1 0.24206600 -2.2937805 0.091 0.167 1 NRBP1 g2:g1
#> HLA-DQA2 0.24489452 0.6449536 0.250 0.139 1 HLA-DQA2 g2:g1
#> SCO2 0.24808905 0.8095112 0.182 0.083 1 SCO2 g2:g1
#> PTPN22 0.25724622 -2.1902685 0.045 0.111 1 PTPN22 g2:g1
#> PPP3CC 0.26106405 0.7908963 0.136 0.056 1 PPP3CC g2:g1
#> ZNF76 0.26360996 1.2855973 0.091 0.028 1 ZNF76 g2:g1
#> CD1C 0.26360996 1.5571143 0.091 0.028 1 CD1C g2:g1
#> WARS 0.26808657 -1.3804565 0.159 0.250 1 WARS g2:g1
#> EPC1 0.27173354 0.8665448 0.205 0.111 1 EPC1 g2:g1
#> TCL1A 0.27307223 -1.8951067 0.068 0.139 1 TCL1A g2:g1
#> CCDC104 0.27358239 0.9099128 0.091 0.028 1 CCDC104 g2:g1
#> GZMH 0.28136356 1.6970640 0.159 0.083 1 GZMH g2:g1
#> HLA-DRA 0.28215715 0.2258141 0.727 0.639 1 HLA-DRA g2:g1
#> RBP7 0.28966268 -1.1441332 0.068 0.139 1 RBP7 g2:g1
#> RGS2 0.29358016 -0.6789153 0.409 0.278 1 RGS2 g2:g1
#> MPHOSPH6 0.29667195 1.4082929 0.159 0.083 1 MPHOSPH6 g2:g1
#> TREML1 0.29820733 -1.3982890 0.068 0.139 1 TREML1 g2:g1
#> TCF7 0.30419782 -0.9406441 0.114 0.194 1 TCF7 g2:g1
#> PTCRA 0.30440015 -0.2643378 0.045 0.111 1 PTCRA g2:g1
#> BLOC1S4 0.30851235 -1.2148305 0.091 0.167 1 BLOC1S4 g2:g1
#> CD9 0.30851235 0.1021292 0.091 0.167 1 CD9 g2:g1
#> TNFRSF1B 0.30987432 0.8275763 0.227 0.139 1 TNFRSF1B g2:g1
#> TPM4 0.31495381 0.4273507 0.409 0.278 1 TPM4 g2:g1
#> LST1 0.32907845 0.1394113 0.500 0.361 1 LST1 g2:g1
#> FAM96A 0.33150327 -0.4500508 0.205 0.111 1 FAM96A g2:g1
#> SERPINA1 0.33384685 0.8580429 0.341 0.250 1 SERPINA1 g2:g1
#> C12orf75 0.34229821 -0.5783239 0.114 0.194 1 C12orf75 g2:g1
#> HLA-DRB1 0.34667535 0.3435079 0.568 0.444 1 HLA-DRB1 g2:g1
#> HLA-DPA1 0.35432386 0.6422033 0.545 0.500 1 HLA-DPA1 g2:g1
#> CARD16 0.35475812 0.1396680 0.409 0.278 1 CARD16 g2:g1
#> HLA-DRB5 0.35956376 0.1505533 0.523 0.361 1 HLA-DRB5 g2:g1
#> ZFP36L1 0.36236507 -2.0075334 0.136 0.194 1 ZFP36L1 g2:g1
#> RHOC 0.36735744 -0.2360902 0.409 0.250 1 RHOC g2:g1
#> CD247 0.37584672 0.4950876 0.250 0.167 1 CD247 g2:g1
#> CFP 0.38055093 -0.4032603 0.364 0.250 1 CFP g2:g1
#> GZMM 0.38163435 0.7040406 0.273 0.194 1 GZMM g2:g1
#> SAT1 0.38637069 0.1496136 0.773 0.639 1 SAT1 g2:g1
#> TALDO1 0.38799801 -1.4821323 0.500 0.500 1 TALDO1 g2:g1
#> YWHAB 0.40132815 0.3123683 0.523 0.528 1 YWHAB g2:g1
#> FPR1 0.40338593 -1.3374693 0.136 0.194 1 FPR1 g2:g1
#> TNFAIP8 0.41017526 -0.6427122 0.250 0.306 1 TNFAIP8 g2:g1
#> TTC38 0.41239096 1.2736847 0.136 0.083 1 TTC38 g2:g1
#> HVCN1 0.41463077 -2.2939901 0.114 0.167 1 HVCN1 g2:g1
#> CCL5 0.41474716 -0.9043819 0.432 0.472 1 CCL5 g2:g1
#> LYZ 0.42215674 0.2979607 0.682 0.583 1 LYZ g2:g1
#> VSTM1 0.42420482 -0.2914488 0.114 0.056 1 VSTM1 g2:g1
#> CD8A 0.42421612 -0.4965425 0.114 0.056 1 CD8A g2:g1
#> LAMP1 0.42538075 -0.5861493 0.205 0.278 1 LAMP1 g2:g1
#> CD200 0.43621807 -2.5445648 0.023 0.056 1 CD200 g2:g1
#> CD19 0.44237088 -1.0048143 0.068 0.028 1 CD19 g2:g1
#> DLGAP1-AS1 0.44237088 0.5505892 0.068 0.028 1 DLGAP1-AS1 g2:g1
#> FCER2 0.45379221 -1.7096009 0.045 0.083 1 FCER2 g2:g1
#> FCRLA 0.45379221 -2.2473152 0.045 0.083 1 FCRLA g2:g1
#> TMEM40 0.45934038 -1.4708196 0.068 0.111 1 TMEM40 g2:g1
#> ASGR1 0.46444068 1.3781397 0.136 0.083 1 ASGR1 g2:g1
#> MMADHC 0.46691934 -1.2601668 0.205 0.250 1 MMADHC g2:g1
#> RP11-693J15.5 0.46780299 -1.9053842 0.045 0.083 1 RP11-693J15.5 g2:g1
#> IGLL5 0.47162751 -0.2402105 0.023 0.056 1 IGLL5 g2:g1
#> ANXA2 0.47261188 0.1269778 0.614 0.444 1 ANXA2 g2:g1
#> S1PR4 0.47993990 1.7654906 0.273 0.194 1 S1PR4 g2:g1
#> MYL9 0.48363363 -0.9581845 0.068 0.111 1 MYL9 g2:g1
#> COPS6 0.49620744 -0.8663350 0.273 0.194 1 COPS6 g2:g1
#> FCN1 0.49830814 -0.5499683 0.386 0.417 1 FCN1 g2:g1
#> CD68 0.49979451 0.4068668 0.295 0.222 1 CD68 g2:g1
#> SP100 0.50025570 -0.5112157 0.295 0.194 1 SP100 g2:g1
#> CD79A 0.50287239 -0.6183097 0.136 0.194 1 CD79A g2:g1
#> GPX1 0.51192812 -0.6122229 0.682 0.639 1 GPX1 g2:g1
#> CCR7 0.51836193 1.9506907 0.091 0.056 1 CCR7 g2:g1
#> ADAR 0.52877864 -0.1155165 0.182 0.222 1 ADAR g2:g1
#> ACRBP 0.53424169 0.8715893 0.068 0.111 1 ACRBP g2:g1
#> FGFBP2 0.53811724 1.3991481 0.250 0.222 1 FGFBP2 g2:g1
#> TYROBP 0.54258037 0.1047340 0.636 0.500 1 TYROBP g2:g1
#> GP9 0.54308166 -0.2629969 0.091 0.139 1 GP9 g2:g1
#> ODC1 0.54704146 -0.8462178 0.182 0.222 1 ODC1 g2:g1
#> MS4A1 0.54893336 -1.7447339 0.136 0.167 1 MS4A1 g2:g1
#> KLRD1 0.55544738 0.5675050 0.159 0.111 1 KLRD1 g2:g1
#> LY86 0.56056635 0.1599974 0.250 0.194 1 LY86 g2:g1
#> NFKBIA 0.56488054 0.6054230 0.591 0.472 1 NFKBIA g2:g1
#> NKG7 0.56823957 0.2819263 0.477 0.389 1 NKG7 g2:g1
#> DNAJB1 0.57140408 -0.2655006 0.227 0.278 1 DNAJB1 g2:g1
#> LCK 0.57352870 0.3533948 0.318 0.250 1 LCK g2:g1
#> MPEG1 0.57892640 -0.7608735 0.205 0.139 1 MPEG1 g2:g1
#> SMCO4 0.58895599 -0.3460177 0.205 0.139 1 SMCO4 g2:g1
#> IL1B 0.60418281 1.0822189 0.205 0.167 1 IL1B g2:g1
#> AIF1 0.60882656 0.1259509 0.545 0.444 1 AIF1 g2:g1
#> HNRNPA3 0.60921704 -0.1623689 0.409 0.306 1 HNRNPA3 g2:g1
#> AKR1C3 0.61597272 0.9619857 0.114 0.083 1 AKR1C3 g2:g1
#> CD14 0.61951529 -1.2948842 0.159 0.194 1 CD14 g2:g1
#> CD3E 0.62522103 0.4977330 0.341 0.278 1 CD3E g2:g1
#> GNG11 0.63742523 -1.1347009 0.114 0.139 1 GNG11 g2:g1
#> CLIC3 0.64234460 0.9081385 0.114 0.083 1 CLIC3 g2:g1
#> CLU 0.64949087 -0.9996102 0.114 0.139 1 CLU g2:g1
#> CTSW 0.65028217 -0.3922628 0.341 0.250 1 CTSW g2:g1
#> STX10 0.65074656 -0.7783398 0.159 0.194 1 STX10 g2:g1
#> GZMK 0.66243894 -1.7574529 0.091 0.111 1 GZMK g2:g1
#> IL7R 0.66674361 0.2082191 0.341 0.333 1 IL7R g2:g1
#> PTGDR 0.66918992 -2.7669811 0.114 0.083 1 PTGDR g2:g1
#> S100B 0.67009042 4.1497946 0.045 0.028 1 S100B g2:g1
#> LILRA3 0.67596773 -1.9791945 0.091 0.111 1 LILRA3 g2:g1
#> DNAJC2 0.67885156 -0.1544783 0.182 0.139 1 DNAJC2 g2:g1
#> GYPC 0.68005668 -0.8651684 0.250 0.278 1 GYPC g2:g1
#> MYO1G 0.68065858 0.6695113 0.409 0.333 1 MYO1G g2:g1
#> IL2RB 0.68277191 0.2945914 0.114 0.083 1 IL2RB g2:g1
#> PPP1R18 0.68939101 0.3244785 0.318 0.278 1 PPP1R18 g2:g1
#> NT5C 0.70343211 -1.2694963 0.227 0.167 1 NT5C g2:g1
#> S100A11 0.70479142 0.1499056 0.591 0.528 1 S100A11 g2:g1
#> XBP1 0.71198923 0.1016697 0.318 0.250 1 XBP1 g2:g1
#> TMEM204 0.71342360 0.4482229 0.045 0.028 1 TMEM204 g2:g1
#> S100A8 0.71501151 -1.2624184 0.409 0.306 1 S100A8 g2:g1
#> NCOA4 0.73091444 -0.8719660 0.250 0.194 1 NCOA4 g2:g1
#> PGRMC1 0.73809476 -0.4498943 0.114 0.083 1 PGRMC1 g2:g1
#> CTSB 0.73923287 -0.6614962 0.318 0.250 1 CTSB g2:g1
#> IGFBP7 0.75069884 -0.5043795 0.205 0.222 1 IGFBP7 g2:g1
#> CD79B 0.76680522 -1.2150744 0.295 0.278 1 CD79B g2:g1
#> SATB1 0.76687418 -3.0600459 0.068 0.083 1 SATB1 g2:g1
#> RP11-290F20.3 0.76832326 0.1220792 0.136 0.111 1 RP11-290F20.3 g2:g1
#> HLA-DMB 0.77306125 -0.3343191 0.341 0.278 1 HLA-DMB g2:g1
#> CD2 0.77334050 0.5941658 0.159 0.139 1 CD2 g2:g1
#> PIK3IP1 0.77930880 1.4533085 0.159 0.139 1 PIK3IP1 g2:g1
#> GZMA 0.78049937 -0.1186839 0.227 0.250 1 GZMA g2:g1
#> PMPCB 0.78121854 0.1265535 0.136 0.111 1 PMPCB g2:g1
#> KIAA0125 0.80780244 -1.8552812 0.045 0.056 1 KIAA0125 g2:g1
#> CYB561A3 0.80780244 -1.8289438 0.045 0.056 1 CYB561A3 g2:g1
#> CD180 0.80780244 -1.5002871 0.045 0.056 1 CD180 g2:g1
#> HNRNPH1 0.82024117 -0.2902894 0.136 0.111 1 HNRNPH1 g2:g1
#> IL32 0.82066860 -0.5310219 0.295 0.306 1 IL32 g2:g1
#> ASNSD1 0.82403692 -0.2054350 0.068 0.083 1 ASNSD1 g2:g1
#> MAL 0.83229313 0.2357011 0.068 0.083 1 MAL g2:g1
#> LINC00926 0.84467238 -0.3201780 0.068 0.056 1 LINC00926 g2:g1
#> PPBP 0.85072316 -0.8161701 0.159 0.167 1 PPBP g2:g1
#> HNRNPF 0.85270253 -0.1318392 0.432 0.361 1 HNRNPF g2:g1
#> IL17RA 0.86275280 -1.1075541 0.068 0.056 1 IL17RA g2:g1
#> SRSF7 0.87608406 -1.5599110 0.500 0.472 1 SRSF7 g2:g1
#> POP7 0.87628706 1.5192430 0.159 0.139 1 POP7 g2:g1
#> PPAPDC1B 0.88090539 -0.8740292 0.068 0.056 1 PPAPDC1B g2:g1
#> NRGN 0.88965687 0.1178269 0.182 0.167 1 NRGN g2:g1
#> XCL2 0.89794707 0.3356016 0.091 0.083 1 XCL2 g2:g1
#> CFD 0.90550039 -0.4594260 0.273 0.250 1 CFD g2:g1
#> ITGA2B 0.90877741 -1.4419882 0.114 0.111 1 ITGA2B g2:g1
#> LDHB 0.90895712 -0.1769172 0.523 0.444 1 LDHB g2:g1
#> SDPR 0.91637557 -0.7586314 0.136 0.139 1 SDPR g2:g1
#> EIF4A2 0.92216620 -0.1168652 0.523 0.500 1 EIF4A2 g2:g1
#> SPARC 0.92920397 -0.6536246 0.136 0.139 1 SPARC g2:g1
#> S100A9 0.93413505 -0.7924142 0.386 0.389 1 S100A9 g2:g1
#> EAF2 0.93677400 -2.6687209 0.114 0.111 1 EAF2 g2:g1
#> KHDRBS1 0.94760219 -2.8736243 0.182 0.167 1 KHDRBS1 g2:g1
#> C5AR1 0.95034695 -0.9861914 0.159 0.139 1 C5AR1 g2:g1
#> HLA-DPB1 0.95531585 0.2193854 0.523 0.556 1 HLA-DPB1 g2:g1
#> TYMP 0.95715084 -0.1454613 0.432 0.417 1 TYMP g2:g1
#> CRBN 0.95942509 -0.8320513 0.273 0.222 1 CRBN g2:g1
#> CTSS 0.96412214 0.1540970 0.591 0.611 1 CTSS g2:g1
#> KLRG1 0.96484898 -0.3207581 0.114 0.111 1 KLRG1 g2:g1
#> MS4A6A 0.98895497 -0.5252983 0.205 0.194 1 MS4A6A g2:g1
#> NGFRAP1 0.99296761 -0.6881485 0.114 0.111 1 NGFRAP1 g2:g1
#> CA2 0.99296761 0.8072664 0.114 0.111 1 CA2 g2:g1
#> CD3D 0.99517096 -0.5121695 0.295 0.278 1 CD3D g2:g1
#> RARRES3 0.99556237 0.1837819 0.364 0.389 1 RARRES3 g2:g1