Returns averaged expression values for each identity class

AverageExpression(
  object,
  assays = NULL,
  features = NULL,
  return.seurat = FALSE,
  group.by = "ident",
  add.ident = NULL,
  slot = "data",
  verbose = TRUE,
  ...
)

Arguments

object

Seurat object

assays

Which assays to use. Default is all assays

features

Features to analyze. Default is all features in the assay

return.seurat

Whether to return the data as a Seurat object. Default is FALSE

group.by

Categories for grouping (e.g, ident, replicate, celltype); 'ident' by default

add.ident

(Deprecated) Place an additional label on each cell prior to pseudobulking (very useful if you want to observe cluster pseudobulk values, separated by replicate, for example)

slot

Slot(s) to use; if multiple slots are given, assumed to follow the order of 'assays' (if specified) or object's assays

verbose

Print messages and show progress bar

...

Arguments to be passed to methods such as CreateSeuratObject

Value

Returns a matrix with genes as rows, identity classes as columns. If return.seurat is TRUE, returns an object of class Seurat.

Details

If slot is set to 'data', this function assumes that the data has been log normalized and therefore feature values are exponentiated prior to averaging so that averaging is done in non-log space. Otherwise, if slot is set to either 'counts' or 'scale.data', no exponentiation is performed prior to averaging If return.seurat = TRUE and slot is not 'scale.data', averaged values are placed in the 'counts' slot of the returned object and the log of averaged values are placed in the 'data' slot. ScaleData is then run on the default assay before returning the object. If return.seurat = TRUE and slot is 'scale.data', the 'counts' slot is left empty, the 'data' slot is filled with NA, and 'scale.data' is set to the aggregated values.

Examples

data("pbmc_small") head(AverageExpression(object = pbmc_small))
#> $RNA #> 0 1 2 #> MS4A1 0.0000000 2.0834431 171.6152133 #> CD79B 10.8146571 17.5488424 152.1344066 #> CD79A 0.0000000 11.6183331 215.0868777 #> HLA-DRA 37.1058569 405.8505224 1158.0852037 #> TCL1A 0.0000000 3.4632035 142.0747887 #> HLA-DQB1 3.9682540 45.3531831 169.2761547 #> HVCN1 0.0000000 5.5493118 74.7840655 #> HLA-DMB 0.6270379 19.7942417 74.2874820 #> LTB 261.9397358 20.8604601 265.6882303 #> LINC00926 0.0000000 0.0000000 30.9424559 #> FCER2 0.0000000 0.0000000 24.5493077 #> SP100 15.6005001 6.1750842 58.2192340 #> NCF1 0.0000000 6.8263157 42.6771926 #> PPP3CC 10.8216892 0.0000000 29.1362189 #> EAF2 0.0000000 2.5180144 40.3994289 #> PPAPDC1B 0.0000000 0.8658009 32.1424635 #> CD19 0.0000000 0.0000000 33.1904722 #> KIAA0125 0.0000000 0.0000000 26.4562923 #> CYB561A3 0.0000000 0.0000000 27.5709719 #> CD180 0.0000000 0.0000000 23.3758914 #> RP11-693J15.5 0.0000000 0.8658009 30.6821544 #> FAM96A 11.1722196 4.4577227 34.9186269 #> CXCR4 98.3338828 17.8901333 178.7297293 #> STX10 12.5045693 5.8300510 47.2829430 #> SNHG7 12.3074439 3.3061349 42.1701543 #> NT5C 4.1293941 3.6108167 65.3411927 #> BANK1 3.7950664 1.0282776 23.3701089 #> IGLL5 0.0000000 0.0000000 176.3232916 #> CD200 0.0000000 0.0000000 22.7075173 #> FCRLA 0.0000000 1.7316017 24.3058412 #> CD3D 153.5649197 0.8639309 127.0331731 #> NOSIP 73.2797394 9.0948849 7.6324578 #> SAFB2 16.5415100 0.0000000 0.0000000 #> CD2 42.1834786 0.5641749 10.3604644 #> IL7R 141.5908000 8.9462345 27.5432225 #> PIK3IP1 53.6527986 2.0360790 13.1724647 #> MPHOSPH6 25.3937763 2.3014087 3.7864445 #> KHDRBS1 72.0846330 3.8116218 2.6683984 #> MAL 16.0592569 1.0335917 0.0000000 #> CCR7 30.5272533 0.0000000 4.8285852 #> THYN1 34.1835381 1.9420980 4.2736648 #> TAF7 49.8036523 9.7831629 18.7491113 #> LDHB 123.7740433 22.4662941 69.9088096 #> TMEM123 73.5008600 14.7925494 48.3924124 #> CCDC104 12.2007319 0.0000000 4.2736648 #> EPC1 25.7422982 1.9184652 15.1113784 #> EIF4A2 128.1660254 18.6724383 72.4657157 #> CD3E 94.2411782 1.3422819 35.0592588 #> TMUB1 17.9154372 4.3086117 0.0000000 #> BLOC1S4 21.8578141 3.5277239 0.0000000 #> ACSM3 12.1098536 0.0000000 0.0000000 #> TMEM204 10.6040564 0.0000000 0.0000000 #> SRSF7 181.6092692 35.4752721 38.2142627 #> ACAP1 45.9035370 0.0000000 3.3591532 #> TNFAIP8 41.2141455 6.4144652 24.1945212 #> CD7 92.2752707 0.0000000 14.4498615 #> TAGAP 27.1580878 5.5600733 17.9769170 #> DNAJB1 40.4013422 8.6478486 7.5728891 #> ASNSD1 17.2698485 1.7167382 0.0000000 #> S1PR4 72.3405851 5.0372914 18.1405196 #> CTSW 86.7093191 1.0282776 51.7081787 #> GZMK 28.0274014 0.0000000 14.5700621 #> NKG7 512.8914342 22.0674777 258.4848943 #> IL32 177.4325769 3.7481188 58.9841613 #> DNAJC2 13.9224520 3.0907194 12.8961274 #> LYAR 47.0389185 5.5948469 188.9277890 #> CST7 102.6754272 1.9064568 43.8446120 #> LCK 65.8374079 0.7968127 22.0894637 #> CCL5 406.7622694 11.0377053 195.6632380 #> HNRNPH1 14.0128491 0.0000000 10.1346582 #> SSR2 88.3861651 25.8401080 53.0763673 #> DLGAP1-AS1 5.9481187 0.0000000 3.6049027 #> GIMAP1 69.2229891 11.9834749 5.0587798 #> MMADHC 17.0508955 4.9502520 28.4541742 #> ZNF76 6.1724389 0.9852217 3.6049027 #> CD8A 19.0675035 0.0000000 19.4851205 #> PTPN22 9.9284108 1.1080332 6.9192766 #> GYPC 72.6410338 1.1080332 24.8615048 #> HNRNPF 56.2569207 8.3439560 37.7838061 #> RPL7L1 12.5615300 3.3095509 14.7269828 #> KLRG1 34.3723933 0.0000000 3.7864445 #> CRBN 22.1006178 3.8728705 28.2132364 #> SATB1 44.6865377 0.0000000 4.4552066 #> SIT1 9.3470842 0.0000000 22.2153245 #> PMPCB 7.6908759 1.9928243 17.4507663 #> NRBP1 17.1156102 1.1331445 8.0601093 #> TCF7 23.7993821 0.5369128 10.6341475 #> HNRNPA3 33.9362413 11.1442131 36.6321466 #> S100A8 4.9650245 336.9712070 0.6035732 #> S100A9 18.7726466 656.1327572 5.6267095 #> LYZ 44.3166692 987.1410022 262.0950959 #> CD14 0.0000000 26.2034214 1.2071463 #> FCN1 22.2339539 120.6601510 34.1491283 #> TYROBP 109.2251513 358.4089463 31.4775288 #> ASGR1 0.0000000 11.6507481 0.6980316 #> NFKBIA 40.3551279 94.2730751 45.4429752 #> TYMP 8.5907702 120.5213230 19.3778870 #> CTSS 48.7494247 206.0390043 80.1845419 #> TSPO 27.2968127 121.0927239 28.0120931 #> RBP7 0.0000000 17.0683782 6.6622252 #> CTSB 5.0909681 42.2256517 4.4552066 #> LGALS1 89.1253535 323.0851850 109.9532830 #> FPR1 0.6270379 19.6836961 0.0000000 #> VSTM1 0.6270379 8.6799017 0.0000000 #> BLVRA 10.2053899 32.7495715 13.1200667 #> MPEG1 0.5270926 15.4504481 8.2584587 #> BID 8.3159934 61.1706349 10.2005619 #> SMCO4 0.0000000 18.3329748 3.7864445 #> CFD 5.1490875 65.3697594 11.9629067 #> LINC00936 8.1561448 28.4737760 8.4421203 #> LGALS2 6.9122942 65.8571844 9.8454601 #> MS4A6A 0.0000000 35.0271610 10.6865051 #> FCGRT 6.6727895 56.5610638 5.3075273 #> LGALS3 8.4439161 52.7662602 5.4617039 #> NUP214 3.2679739 23.2488624 1.8402650 #> SCO2 1.2540757 16.4105042 4.2841031 #> IL17RA 0.0000000 9.1053226 0.0000000 #> IFI6 19.7283090 57.5773537 3.6214389 #> HLA-DPA1 12.4868707 229.5861593 343.4057148 #> FCER1A 1.7806268 23.3089669 19.2093092 #> CLEC10A 0.0000000 20.2965208 5.5857079 #> HLA-DMA 4.9734748 40.1660976 52.1950830 #> RGS1 4.3402778 7.7613777 5.2426145 #> HLA-DPB1 6.0767799 244.7304494 602.0288064 #> HLA-DQA1 2.1872266 57.9784339 145.0725831 #> RNF130 2.8597276 29.1769083 2.6391289 #> HLA-DRB5 5.5943535 97.9159755 181.6500690 #> HLA-DRB1 6.1981797 199.1281870 452.2970007 #> CST3 45.7354352 599.2053066 247.0582232 #> IL1B 1.6534392 44.4464822 1.2723353 #> POP7 5.0567120 36.0674619 3.9343597 #> HLA-DQA2 0.0000000 15.0500829 40.0012173 #> CD1C 0.0000000 4.9604985 3.8462753 #> GSTP1 23.5577774 95.0193380 59.0152372 #> EIF3G 53.2294156 38.5381043 45.9356457 #> VPS28 25.5271076 47.5342614 19.2167697 #> LY86 1.3102725 9.7029106 55.1058343 #> ZFP36L1 11.7218366 15.1137006 14.5349240 #> ZNF330 1.7806268 34.1243965 5.9141833 #> ANXA2 42.0551269 68.1518395 42.8037437 #> GRN 6.7640746 48.2384947 14.3070408 #> CFP 8.3765829 59.2776697 19.0165168 #> HSP90AA1 83.3471887 20.6927962 112.4274996 #> FUOM 2.7777778 3.8338913 2.4438382 #> LST1 32.3650271 277.5261364 66.8775564 #> AIF1 44.1995361 273.1165147 59.1440920 #> PSAP 51.2467383 133.0397029 56.3360025 #> YWHAB 38.6195281 72.9875143 45.5779460 #> MYO1G 21.9930278 53.4571904 27.1310876 #> SAT1 117.4983001 326.3858717 76.1437446 #> RGS2 15.6995306 46.0614018 73.7461966 #> SERPINA1 5.0191403 58.6957612 8.2860703 #> IFITM3 9.4632268 95.5734723 21.3350591 #> FCGR3A 45.0575037 67.0556748 15.6953427 #> LILRA3 0.6270379 6.3457005 11.3593336 #> S100A11 49.0681367 175.6737977 35.7881594 #> FCER1G 83.4538796 238.3485366 31.5171587 #> TNFRSF1B 4.0885364 15.6620565 7.9380877 #> IFITM2 175.2043525 157.0332861 111.5103658 #> WARS 8.0281659 17.7774080 11.1777917 #> IFI30 3.7622272 39.6212698 12.9290671 #> MS4A7 3.4413023 17.1919037 11.8359012 #> C5AR1 0.0000000 21.4333574 7.5728891 #> HCK 3.1351894 26.9343385 3.3956994 #> COTL1 83.8340060 298.1075275 135.1491884 #> LGALS9 7.3344097 20.3836895 2.5382965 #> CD68 9.8557636 44.7110882 9.6647083 #> RP11-290F20.3 5.7009995 19.9519703 3.8986355 #> RHOC 27.6135109 32.5258906 7.5177676 #> CARD16 14.6727643 45.4663959 16.7879868 #> LRRC25 1.2540757 19.4130703 17.3426901 #> COPS6 20.2274673 36.1064364 4.3900177 #> ADAR 10.5679462 37.3094760 23.5241672 #> PPBP 563.6202644 11.1643601 2.7555800 #> GPX1 219.8601031 137.9965947 53.5929229 #> TPM4 51.7217276 10.3705233 10.4456613 #> PF4 192.0248681 0.0000000 1.8402650 #> SDPR 100.3673346 3.4334764 0.6980316 #> NRGN 33.8803910 8.1703970 0.0000000 #> SPARC 46.5190018 4.5666209 0.0000000 #> GNG11 112.1841619 1.7167382 0.0000000 #> CLU 95.7016028 3.4334764 0.0000000 #> HIST1H2AC 59.0750748 1.7167382 3.8986355 #> NCOA4 71.6604309 7.1561419 5.0587798 #> GP9 45.8668495 0.0000000 0.0000000 #> FERMT3 48.3241454 9.8936936 4.4844761 #> ODC1 34.9215692 4.1286308 9.6562995 #> CD9 81.5036796 5.1948052 0.0000000 #> RUFY1 25.9622868 1.0335917 10.8136685 #> TUBB1 75.7553056 0.0000000 0.0000000 #> TALDO1 87.8624787 49.1675633 15.4575299 #> TREML1 37.3125019 3.4334764 0.0000000 #> NGFRAP1 30.4702497 0.0000000 0.0000000 #> PGRMC1 25.1643084 0.0000000 0.0000000 #> CA2 48.0584353 1.2195122 0.0000000 #> ITGA2B 30.0958312 1.1331445 0.0000000 #> MYL9 28.5163692 1.7167382 0.0000000 #> TMEM40 19.0248410 0.0000000 0.0000000 #> PARVB 21.3308930 3.3156187 3.7864445 #> PTCRA 27.9168501 0.0000000 0.0000000 #> ACRBP 27.2689871 1.7167382 0.0000000 #> TSC22D1 26.3229303 1.7167382 0.0000000 #> VDAC3 89.8938572 4.7474053 80.5805836 #> GZMB 134.7525767 3.2398045 9.1533181 #> GZMA 132.0877530 1.3698630 53.1748514 #> GNLY 303.8483826 0.7968127 2.5382965 #> FGFBP2 99.7206648 5.2636456 33.5469581 #> AKR1C3 29.2797250 0.0000000 0.0000000 #> CCL4 27.5128591 1.3422819 13.7299771 #> PRF1 139.3017391 1.3698630 55.6407029 #> GZMH 71.8802761 0.0000000 13.7299771 #> XBP1 47.7346291 3.2819082 13.3173223 #> GZMM 54.4592898 0.0000000 26.3667455 #> PTGDR 51.7749811 0.0000000 8.1815617 #> IGFBP7 31.8683451 11.8421373 1.8107195 #> TTC38 11.3346912 0.9029345 4.5766590 #> KLRD1 19.8899977 1.1080332 0.0000000 #> ARHGDIA 36.8782529 17.3405284 21.2707611 #> IL2RB 15.0729130 0.0000000 3.8986355 #> CLIC3 20.4099139 1.0335917 5.2110474 #> PPP1R18 35.1094938 6.0370707 36.4916898 #> CD247 39.0664491 1.1331445 8.3631036 #> ALOX5AP 35.9601264 4.2811014 37.4487754 #> XCL2 12.7043849 0.0000000 8.3631036 #> C12orf75 24.1229940 0.5369128 9.0318657 #> RARRES3 75.8379678 4.7837931 43.4589512 #> PCMT1 96.1552660 16.9819608 8.2362929 #> LAMP1 49.3565581 1.5705045 3.7864445 #> SPON2 38.2714225 2.7370379 23.5520573 #> S100B 20.5248993 0.0000000 0.0000000 #>