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