Users have to run runDEAnalysis() first, any of the
wrapped functions of this generic function. Users can set further filters on
the result. A data.frame object, with variables of Gene,
Log2_FC, Pvalue, and FDR, will be returned.
getDEGTopTable(
inSCE,
useResult,
labelBy = S4Vectors::metadata(inSCE)$featureDisplay,
onlyPos = FALSE,
log2fcThreshold = 0.25,
fdrThreshold = 0.05,
minGroup1MeanExp = NULL,
maxGroup2MeanExp = NULL,
minGroup1ExprPerc = NULL,
maxGroup2ExprPerc = NULL
)SingleCellExperiment inherited object, with of the singleCellTK DEG method performed in advance.
character. A string specifying the analysisName
used when running a differential expression analysis function.
A single character for a column of rowData(inSCE) as
where to search for the labeling text. Leave NULL for rownames.
Default metadata(inSCE)$featureDisplay (see
setSCTKDisplayRow).
logical. Whether to only fetch DEG with positive log2_FC
value. Default FALSE.
numeric. Only fetch DEGs with the absolute values of
log2FC larger than this value. Default 0.25.
numeric. Only fetch DEGs with FDR value smaller than this
value. Default 0.05.
numeric. Only fetch DEGs with mean expression in
group1 greater then this value. Default NULL.
numeric. Only fetch DEGs with mean expression in
group2 less then this value. Default NULL.
numeric. Only fetch DEGs expressed in greater then
this fraction of cells in group1. Default NULL.
numeric. Only fetch DEGs expressed in less then this
fraction of cells in group2. Default NULL.
A data.frame object of the top DEGs, with variables of
Gene, Log2_FC, Pvalue, and FDR.
data("sceBatches")
sceBatches <- scaterlogNormCounts(sceBatches, "logcounts")
sce.w <- subsetSCECols(sceBatches, colData = "batch == 'w'")
sce.w <- runWilcox(sce.w, class = "cell_type", classGroup1 = "alpha",
groupName1 = "w.alpha", groupName2 = "w.beta",
analysisName = "w.aVSb")
#> Sat Mar 18 10:27:48 2023 ... Running DE with wilcox, Analysis name: w.aVSb
getDEGTopTable(sce.w, "w.aVSb")
#> Gene Log2_FC Pvalue FDR group1MeanExp
#> 2 GCG 9.1517909 2.368614e-19 4.737227e-18 18.2513675
#> 48 GC 7.1878882 4.658205e-15 5.822756e-14 8.7962925
#> 9 TM4SF4 6.4072019 2.739759e-13 2.490690e-12 10.2257508
#> 72 RGS4 5.4637919 9.524267e-10 6.349511e-09 9.3192184
#> 61 PDK4 4.5360064 2.535638e-07 1.056516e-06 8.4809718
#> 88 TTR 4.3825672 3.348780e-17 4.783971e-16 16.0047494
#> 68 SERPINA1 2.9853497 2.218207e-04 5.837387e-04 7.0352827
#> 78 KCNQ1OT1 2.6699417 6.608041e-04 1.501827e-03 6.0075125
#> 11 PENK 0.9654197 1.754329e-02 3.189689e-02 1.0147027
#> 97 SNX22 -1.1238276 3.454043e-03 6.908086e-03 7.8894950
#> 81 PKM2 -1.1729284 6.785609e-03 1.330512e-02 7.3410304
#> 96 C11orf10 -1.2673860 4.634275e-04 1.077738e-03 7.1695226
#> 73 FOS -1.3535129 1.823620e-02 3.256465e-02 8.2410871
#> 64 C6orf62 -1.4303264 1.776495e-03 3.779777e-03 10.1448315
#> 85 C10orf58 -1.6580742 8.496465e-03 1.603107e-02 5.4053757
#> 40 VCAN -1.6914180 2.586650e-04 6.632435e-04 0.1348696
#> 18 NM-001166106 -1.7095593 4.756783e-07 1.902713e-06 9.7766808
#> 43 MLL3 -1.7807672 4.587914e-04 1.077738e-03 7.7422834
#> 98 RPL17-C18ORF32 -1.7895368 8.133631e-06 2.804700e-05 6.8208473
#> 69 MLL -1.8153392 1.348475e-03 2.996612e-03 5.9892851
#> 70 TUBA1A -1.8223863 4.544070e-05 1.336491e-04 9.5849051
#> 87 KIAA0494 -1.8671111 2.676761e-02 4.696072e-02 4.5435264
#> 75 ROD1 -1.8832646 7.790889e-03 1.498248e-02 5.2421307
#> 20 EGR1 -2.0661563 3.793268e-04 9.251873e-04 9.0059561
#> 33 CHP -2.0821137 2.684848e-04 6.712119e-04 8.0260864
#> 44 SRSF6 -2.0881730 1.189004e-05 3.835497e-05 9.5833679
#> 83 FLJ43390 -2.1821390 1.284192e-02 2.378134e-02 4.1766723
#> 99 TTC35 -2.2703597 1.915506e-03 3.990638e-03 3.9697651
#> 51 C2orf28 -2.3401725 1.039625e-04 2.809797e-04 6.7207090
#> 80 MLL5 -2.3693014 6.750971e-06 2.411061e-05 6.9113917
#> 79 TMEM85 -2.5089275 1.018119e-05 3.393730e-05 5.6858668
#> 63 LOC729013 -2.5631018 1.561273e-03 3.394072e-03 4.2301904
#> 39 RIN2 -2.6455051 1.481920e-06 5.488594e-06 9.2894285
#> 52 C14orf43 -2.6597468 2.774656e-03 5.662562e-03 4.0551095
#> 71 TLK1 -2.7498540 1.541148e-07 6.700642e-07 8.9463780
#> 32 SEC22B -2.7715616 2.049612e-09 1.281007e-08 8.3433933
#> 26 LOC647979 -2.9204542 2.744513e-09 1.614419e-08 8.6952640
#> 66 C9orf5 -2.9296536 3.752854e-05 1.172767e-04 4.9630843
#> 22 SLC30A8 -3.0773276 1.216120e-08 6.080598e-08 9.5767369
#> 77 ZNF252 -3.1415988 6.620272e-05 1.838964e-04 2.7664542
#> 59 SC5DL -3.2686407 4.937434e-05 1.410695e-04 4.8721506
#> 56 PTEN -3.3372373 3.758369e-10 2.684550e-09 9.0773050
#> 53 ETNK1 -3.4238773 8.381062e-08 3.990982e-07 8.5213021
#> 67 FAM18B1 -3.4609207 5.739256e-09 3.020661e-08 5.7486900
#> 46 DPYSL2 -3.6028768 3.064074e-10 2.356980e-09 8.6913722
#> 100 C8orf83 -3.7073784 6.952554e-07 2.674059e-06 3.3887995
#> 89 SCGN -3.8122943 3.019451e-14 3.354946e-13 8.7238794
#> 47 TSIX -3.9086902 4.398954e-05 1.333016e-04 2.6458110
#> 34 MAP1B -4.0106181 6.802842e-14 6.802842e-13 9.4915049
#> 28 C10orf46 -4.1172723 1.264781e-07 5.749006e-07 6.0973324
#> 37 G6PC2 -4.5526717 4.065000e-09 2.258333e-08 6.6388158
#> 86 RBP4 -5.5673377 4.757801e-11 3.964834e-10 0.6734410
#> 74 ADCYAP1 -9.5222344 3.683325e-21 3.683325e-19 0.4903626
#> 57 HADH -10.5612840 6.226069e-20 3.113034e-18 1.3295260
#> 16 IAPP -11.3726919 1.027650e-17 1.712751e-16 2.8707631
#> 1 INS -12.7028733 2.368614e-19 4.737227e-18 3.9112870
#> 29 INS-IGF2 -12.9324068 2.367422e-19 4.737227e-18 3.1557017
#> group2MeanExp group1ExprPerc group2ExprPerc
#> 2 9.09957654 1.0000000 1.000
#> 48 1.60840430 0.9529412 0.550
#> 9 3.81854893 0.9647059 0.950
#> 72 3.85542656 0.9882353 0.675
#> 61 3.94496542 0.9411765 0.725
#> 88 11.62218219 1.0000000 0.950
#> 68 4.04993303 0.9176471 0.775
#> 78 3.33757081 0.8235294 0.600
#> 11 0.04928302 0.1764706 0.025
#> 97 9.01332262 0.9764706 1.000
#> 81 8.51395886 0.9529412 1.000
#> 96 8.43690863 0.9764706 0.975
#> 73 9.59460002 0.9411765 0.925
#> 64 11.57515787 1.0000000 1.000
#> 85 7.06344991 0.8352941 0.900
#> 40 1.82628761 0.1058824 0.350
#> 18 11.48624002 1.0000000 1.000
#> 43 9.52305067 0.9647059 0.975
#> 98 8.61038416 0.9882353 0.975
#> 69 7.80462426 0.9058824 0.950
#> 70 11.40729140 0.9882353 1.000
#> 87 6.41063752 0.8235294 0.850
#> 75 7.12539527 0.8941176 0.900
#> 20 11.07211242 0.9647059 0.950
#> 33 10.10820003 0.9647059 1.000
#> 44 11.67154094 0.9882353 1.000
#> 83 6.35881128 0.8000000 0.775
#> 99 6.24012476 0.7294118 0.875
#> 51 9.06088151 0.8705882 0.975
#> 80 9.28069305 0.9529412 1.000
#> 79 8.19479424 0.8823529 0.950
#> 63 6.79329220 0.6117647 0.850
#> 39 11.93493359 0.9529412 1.000
#> 52 6.71485637 0.6941176 0.850
#> 71 11.69623200 0.9882353 1.000
#> 32 11.11495483 1.0000000 1.000
#> 26 11.61571820 1.0000000 1.000
#> 66 7.89273792 0.8235294 0.900
#> 22 12.65406454 0.9764706 1.000
#> 77 5.90805298 0.5294118 0.825
#> 59 8.14079126 0.8352941 0.875
#> 56 12.41454230 0.9882353 1.000
#> 53 11.94517933 0.9764706 1.000
#> 67 9.20961064 0.8352941 0.975
#> 46 12.29424906 1.0000000 1.000
#> 100 7.09617794 0.6705882 0.925
#> 89 12.53617374 0.9764706 1.000
#> 47 6.55450124 0.4235294 0.725
#> 34 13.50212304 0.9882353 1.000
#> 28 10.21460475 0.8588235 0.925
#> 37 11.19148754 0.8941176 0.975
#> 86 6.24077871 0.3764706 0.800
#> 74 10.01259702 0.3058824 1.000
#> 57 11.89080997 0.5294118 1.000
#> 16 14.24345508 0.8588235 0.975
#> 1 16.61416028 0.9882353 1.000
#> 29 16.08810854 0.9647059 1.000