Returns aggregated (summed) expression values for each identity class

AggregateExpression(
  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 aggregating so that sum is done in non-log space. Otherwise, if slot is set to either 'counts' or 'scale.data', no exponentiation is performed prior to aggregating If return.seurat = TRUE and slot is not 'scale.data', aggregated values are placed in the 'counts' slot of the returned object and the log of aggregated values are placed in the 'data' slot. For the 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(AggregateExpression(object = pbmc_small))
#> $RNA #> 0 1 2 #> MS4A1 0.00000 52.08608 3260.68905 #> CD79B 389.32766 438.72106 2890.55373 #> CD79A 0.00000 290.45833 4086.65068 #> HLA-DRA 1335.81085 10146.26306 22003.61887 #> TCL1A 0.00000 86.58009 2699.42099 #> HLA-DQB1 142.85714 1133.82958 3216.24694 #> HVCN1 0.00000 138.73279 1420.89724 #> HLA-DMB 22.57336 494.85604 1411.46216 #> LTB 9429.83049 521.51150 5048.07638 #> LINC00926 0.00000 0.00000 587.90666 #> FCER2 0.00000 0.00000 466.43685 #> SP100 561.61800 154.37710 1106.16545 #> NCF1 0.00000 170.65789 810.86666 #> PPP3CC 389.58081 0.00000 553.58816 #> EAF2 0.00000 62.95036 767.58915 #> PPAPDC1B 0.00000 21.64502 610.70681 #> CD19 0.00000 0.00000 630.61897 #> KIAA0125 0.00000 0.00000 502.66955 #> CYB561A3 0.00000 0.00000 523.84847 #> CD180 0.00000 0.00000 444.14194 #> RP11-693J15.5 0.00000 21.64502 582.96093 #> FAM96A 402.19990 111.44307 663.45391 #> CXCR4 3540.01978 447.25333 3395.86486 #> STX10 450.16450 145.75128 898.37592 #> SNHG7 443.06798 82.65337 801.23293 #> NT5C 148.65819 90.27042 1241.48266 #> BANK1 136.62239 25.70694 444.03207 #> IGLL5 0.00000 0.00000 3350.14254 #> CD200 0.00000 0.00000 431.44283 #> FCRLA 0.00000 43.29004 461.81098 #> CD3D 5528.33711 21.59827 2413.63029 #> NOSIP 2638.07062 227.37212 145.01670 #> SAFB2 595.49436 0.00000 0.00000 #> CD2 1518.60523 14.10437 196.84882 #> IL7R 5097.26880 223.65586 523.32123 #> PIK3IP1 1931.50075 50.90198 250.27683 #> MPHOSPH6 914.17595 57.53522 71.94245 #> KHDRBS1 2595.04679 95.29054 50.69957 #> MAL 578.13325 25.83979 0.00000 #> CCR7 1098.98112 0.00000 91.74312 #> THYN1 1230.60737 48.55245 81.19963 #> TAF7 1792.93148 244.57907 356.23311 #> LDHB 4455.86556 561.65735 1328.26738 #> TMEM123 2646.03096 369.81373 919.45584 #> CCDC104 439.22635 0.00000 81.19963 #> EPC1 926.72274 47.96163 287.11619 #> EIF4A2 4613.97692 466.81096 1376.84860 #> CD3E 3392.68242 33.55705 666.12592 #> TMUB1 644.95574 107.71529 0.00000 #> BLOC1S4 786.88131 88.19310 0.00000 #> ACSM3 435.95473 0.00000 0.00000 #> TMEM204 381.74603 0.00000 0.00000 #> SRSF7 6537.93369 886.88180 726.07099 #> ACAP1 1652.52733 0.00000 63.82391 #> TNFAIP8 1483.70924 160.36163 459.69590 #> CD7 3321.90975 0.00000 274.54737 #> TAGAP 977.69116 139.00183 341.56142 #> DNAJB1 1454.44832 216.19622 143.88489 #> ASNSD1 621.71454 42.91845 0.00000 #> S1PR4 2604.26106 125.93228 344.66987 #> CTSW 3121.53549 25.70694 982.45540 #> GZMK 1008.98645 0.00000 276.83118 #> NKG7 18464.09163 551.68694 4911.21299 #> IL32 6387.57277 93.70297 1120.69906 #> DNAJC2 501.20827 77.26798 245.02642 #> LYAR 1693.40107 139.87117 3589.62799 #> CST7 3696.31538 47.66142 833.04763 #> LCK 2370.14669 19.92032 419.69981 #> CCL5 14643.44170 275.94263 3717.60152 #> HNRNPH1 504.46257 0.00000 192.55851 #> SSR2 3181.90194 646.00270 1008.45098 #> DLGAP1-AS1 214.13227 0.00000 68.49315 #> GIMAP1 2492.02761 299.58687 96.11682 #> MMADHC 613.83224 123.75630 540.62931 #> ZNF76 222.20780 24.63054 68.49315 #> CD8A 686.43013 0.00000 370.21729 #> PTPN22 357.42279 27.70083 131.46626 #> GYPC 2615.07722 27.70083 472.36859 #> HNRNPF 2025.24914 208.59890 717.89231 #> RPL7L1 452.21508 82.73877 279.81267 #> KLRG1 1237.40616 0.00000 71.94245 #> CRBN 795.62224 96.82176 536.05149 #> SATB1 1608.71536 0.00000 84.64893 #> SIT1 336.49503 0.00000 422.09117 #> PMPCB 276.87153 49.82061 331.56456 #> NRBP1 616.16197 28.32861 153.14208 #> TCF7 856.77775 13.42282 202.04880 #> HNRNPA3 1221.70469 278.60533 696.01078 #> S100A8 178.74088 8424.28018 11.46789 #> S100A9 675.81528 16403.31893 106.90748 #> LYZ 1595.40009 24678.52506 4979.80682 #> CD14 0.00000 655.08553 22.93578 #> FCN1 800.42234 3016.50378 648.83344 #> TYROBP 3932.10545 8960.22366 598.07305 #> ASGR1 0.00000 291.26870 13.26260 #> NFKBIA 1452.78460 2356.82688 863.41653 #> TYMP 309.26773 3013.03308 368.17985 #> CTSS 1754.97929 5150.97511 1523.50630 #> TSPO 982.68526 3027.31810 532.22977 #> RBP7 0.00000 426.70945 126.58228 #> CTSB 183.27485 1055.64129 84.64893 #> LGALS1 3208.51273 8077.12962 2089.11238 #> FPR1 22.57336 492.09240 0.00000 #> VSTM1 22.57336 216.99754 0.00000 #> BLVRA 367.39404 818.73929 249.28127 #> MPEG1 18.97533 386.26120 156.91072 #> BID 299.37576 1529.26587 193.81068 #> SMCO4 0.00000 458.32437 71.94245 #> CFD 185.36715 1634.24399 227.29523 #> LINC00936 293.62121 711.84440 160.40029 #> LGALS2 248.84259 1646.42961 187.06374 #> MS4A6A 0.00000 875.67902 203.04360 #> FCGRT 240.22042 1414.02660 100.84302 #> LGALS3 303.98098 1319.15651 103.77237 #> NUP214 117.64706 581.22156 34.96503 #> SCO2 45.14673 410.26260 81.39796 #> IL17RA 0.00000 227.63307 0.00000 #> IFI6 710.21912 1439.43384 68.80734 #> HLA-DPA1 449.52735 5739.65398 6524.70858 #> FCER1A 64.10256 582.72417 364.97687 #> CLEC10A 0.00000 507.41302 106.12845 #> HLA-DMA 179.04509 1004.15244 991.70658 #> RGS1 156.25000 194.03444 99.60967 #> HLA-DPB1 218.76408 6118.26123 11438.54732 #> HLA-DQA1 78.74016 1449.46085 2756.37908 #> RNF130 102.95020 729.42271 50.14345 #> HLA-DRB5 201.39673 2447.89939 3451.35131 #> HLA-DRB1 223.13447 4978.20467 8593.64301 #> CST3 1646.47567 14980.13267 4694.10624 #> IL1B 59.52381 1111.16205 24.17437 #> POP7 182.04163 901.68655 74.75283 #> HLA-DQA2 0.00000 376.25207 760.02313 #> CD1C 0.00000 124.01246 73.07923 #> GSTP1 848.07999 2375.48345 1121.28951 #> EIF3G 1916.25896 963.45261 872.77727 #> VPS28 918.97587 1188.35653 365.11862 #> LY86 47.16981 242.57276 1047.01085 #> ZFP36L1 421.98612 377.84251 276.16356 #> ZNF330 64.10256 853.10991 112.36948 #> ANXA2 1513.98457 1703.79599 813.27113 #> GRN 243.50668 1205.96237 271.83377 #> CFP 301.55698 1481.94174 361.31382 #> HSP90AA1 3000.49879 517.31991 2136.12249 #> FUOM 100.00000 95.84728 46.43292 #> LST1 1165.14097 6938.15341 1270.67357 #> AIF1 1591.18330 6827.91287 1123.73775 #> PSAP 1844.88258 3325.99257 1070.38405 #> YWHAB 1390.30301 1824.68786 865.98097 #> MYO1G 791.74900 1336.42976 515.49066 #> SAT1 4229.93880 8159.64679 1446.73115 #> RGS2 565.18310 1151.53504 1401.17773 #> SERPINA1 180.68905 1467.39403 157.43534 #> IFITM3 340.67616 2389.33681 405.36612 #> FCGR3A 1622.07013 1676.39187 298.21151 #> LILRA3 22.57336 158.64251 215.82734 #> S100A11 1766.45292 4391.84494 679.97503 #> FCER1G 3004.33967 5958.71342 598.82602 #> TNFRSF1B 147.18731 391.55141 150.82367 #> IFITM2 6307.35669 3925.83215 2118.69695 #> WARS 289.01397 444.43520 212.37804 #> IFI30 135.44018 990.53174 245.65227 #> MS4A7 123.88688 429.79759 224.88212 #> C5AR1 0.00000 535.83394 143.88489 #> HCK 112.86682 673.35846 64.51829 #> COTL1 3018.02421 7452.68819 2567.83458 #> LGALS9 264.03875 509.59224 48.22763 #> CD68 354.80749 1117.77721 183.62946 #> RP11-290F20.3 205.23598 498.79926 74.07407 #> RHOC 994.08639 813.14726 142.83758 #> CARD16 528.21951 1136.65990 318.97175 #> LRRC25 45.14673 485.32676 329.51111 #> COPS6 728.18882 902.66091 83.41034 #> ADAR 380.44606 932.73690 446.95918 #> PPBP 20290.32952 279.10900 52.35602 #> GPX1 7914.96371 3449.91487 1018.26553 #> TPM4 1861.98219 259.26308 198.46757 #> PF4 6912.89525 0.00000 34.96503 #> SDPR 3613.22405 85.83691 13.26260 #> NRGN 1219.69408 204.25993 0.00000 #> SPARC 1674.68407 114.16552 0.00000 #> GNG11 4038.62983 42.91845 0.00000 #> CLU 3445.25770 85.83691 0.00000 #> HIST1H2AC 2126.70269 42.91845 74.07407 #> NCOA4 2579.77551 178.90355 96.11682 #> GP9 1651.20658 0.00000 0.00000 #> FERMT3 1739.66923 247.34234 85.20505 #> ODC1 1257.17649 103.21577 183.46969 #> CD9 2934.13247 129.87013 0.00000 #> RUFY1 934.64232 25.83979 205.45970 #> TUBB1 2727.19100 0.00000 0.00000 #> TALDO1 3163.04923 1229.18908 293.69307 #> TREML1 1343.25007 85.83691 0.00000 #> NGFRAP1 1096.92899 0.00000 0.00000 #> PGRMC1 905.91510 0.00000 0.00000 #> CA2 1730.10367 30.48780 0.00000 #> ITGA2B 1083.44992 28.32861 0.00000 #> MYL9 1026.58929 42.91845 0.00000 #> TMEM40 684.89427 0.00000 0.00000 #> PARVB 767.91215 82.89047 71.94245 #> PTCRA 1005.00660 0.00000 0.00000 #> ACRBP 981.68353 42.91845 0.00000 #> TSC22D1 947.62549 42.91845 0.00000 #> VDAC3 3236.17886 118.68513 1531.03109 #> GZMB 4851.09276 80.99511 173.91304 #> GZMA 4755.15911 34.24658 1010.32218 #> GNLY 10938.54177 19.92032 48.22763 #> FGFBP2 3589.94393 131.59114 637.39220 #> AKR1C3 1054.07010 0.00000 0.00000 #> CCL4 990.46293 33.55705 260.86957 #> PRF1 5014.86261 34.24658 1057.17336 #> GZMH 2587.68994 0.00000 260.86957 #> XBP1 1718.44665 82.04771 253.02912 #> GZMM 1960.53443 0.00000 500.96816 #> PTGDR 1863.89932 0.00000 155.44967 #> IGFBP7 1147.26042 296.05343 34.40367 #> TTC38 408.04888 22.57336 86.95652 #> KLRD1 716.03992 27.70083 0.00000 #> ARHGDIA 1327.61710 433.51321 404.14446 #> IL2RB 542.62487 0.00000 74.07407 #> CLIC3 734.75690 25.83979 99.00990 #> PPP1R18 1263.94178 150.92677 693.34211 #> CD247 1406.39217 28.32861 158.89897 #> ALOX5AP 1294.56455 107.02753 711.52673 #> XCL2 457.35786 0.00000 158.89897 #> C12orf75 868.42778 13.42282 171.60545 #> RARRES3 2730.16684 119.59483 825.72007 #> PCMT1 3461.58957 424.54902 156.48957 #> LAMP1 1776.83609 39.26261 71.94245 #> SPON2 1377.77121 68.42595 447.48909 #> S100B 738.89638 0.00000 0.00000 #>