find significant DE genes using presto
Usage
findMarkersPresto(
ident1,
ident2 = NULL,
object,
only_pos = FALSE,
min_pct = 0.1,
logfc_threshold = 0.25,
assay = assay
)Arguments
- ident1
cell population 1
- ident2
cell population 2, if NULL use all (default: NULL)
- object
Seurat object
- only_pos
only return positive markers? (default: FALSE)
- min_pct
minimum fraction of cells in either two of the populations (default: 0.1)
- logfc_threshold
minimum x-fold difference (default: 0.25)
- assay
which assay to use in DE testing (e.g. RNA or SCT)
Examples
library(Seurat)
findMarkersPresto(ident1 = "0", ident2 = "1", object = pbmc_small, assay = "RNA")
#> For a (much!) faster implementation of the Wilcoxon Rank Sum Test,
#> (default method for FindMarkers) please install the presto package
#> --------------------------------------------
#> install.packages('devtools')
#> devtools::install_github('immunogenomics/presto')
#> --------------------------------------------
#> After installation of presto, Seurat will automatically use the more
#> efficient implementation (no further action necessary).
#> This message will be shown once per session
#> gene avg_log2FC p_val p_val_adj pct.1 pct.2
#> 1 CD7 11.172163 2.291671e-05 5.270843e-03 0.528 0.00
#> 2 LCK 6.298467 1.179184e-04 2.712123e-02 0.500 0.04
#> 3 CCL5 5.198553 6.564657e-05 1.509871e-02 0.667 0.28
#> 4 NFKBIA -1.223713 1.892762e-04 4.353352e-02 0.278 0.88
#> 5 PSAP -1.375977 5.632116e-05 1.295387e-02 0.417 1.00
#> 6 SAT1 -1.473774 1.394154e-04 3.206554e-02 0.639 1.00
#> 7 FCER1G -1.513784 6.370800e-06 1.465284e-03 0.389 1.00
#> 8 CARD16 -1.630200 8.720825e-05 2.005790e-02 0.139 0.72
#> 9 TYROBP -1.714096 4.686298e-07 1.077848e-04 0.444 1.00
#> 10 LINC00936 -1.800795 4.973217e-05 1.143840e-02 0.083 0.60
#> 11 COTL1 -1.829941 2.124963e-05 4.887414e-03 0.500 0.96
#> 12 S100A11 -1.839553 1.235720e-06 2.842157e-04 0.333 1.00
#> 13 LGALS1 -1.857736 5.123692e-07 1.178449e-04 0.500 1.00
#> 14 GSTP1 -2.010925 1.100905e-05 2.532081e-03 0.333 0.88
#> 15 CTSS -2.078919 8.095594e-07 1.861987e-04 0.361 0.96
#> 16 TSPO -2.148317 8.902375e-06 2.047546e-03 0.333 0.88
#> 17 FCN1 -2.438790 5.418631e-07 1.246285e-04 0.167 0.88
#> 18 AIF1 -2.626718 8.106490e-09 1.864493e-06 0.194 1.00
#> 19 LGALS3 -2.639987 4.816986e-06 1.107907e-03 0.111 0.72
#> 20 CFP -2.819252 6.044000e-06 1.390120e-03 0.083 0.68
#> 21 NUP214 -2.820961 5.481682e-05 1.260787e-02 0.028 0.48
#> 22 GRN -2.829504 7.180762e-07 1.651575e-04 0.083 0.76
#> 23 BID -2.875011 2.976826e-06 6.846699e-04 0.083 0.72
#> 24 HLA-DMA -3.007053 2.689683e-05 6.186270e-03 0.056 0.56
#> 25 CTSB -3.045623 1.993113e-05 4.584160e-03 0.111 0.68
#> 26 FCGRT -3.078474 3.166989e-08 7.284074e-06 0.083 0.84
#> 27 HCK -3.092237 6.751546e-06 1.552856e-03 0.028 0.56
#> 28 LST1 -3.099086 1.969061e-09 4.528840e-07 0.139 0.96
#> 29 LGALS2 -3.247194 9.650274e-06 2.219563e-03 0.056 0.60
#> 30 IFITM3 -3.332581 2.301085e-08 5.292495e-06 0.056 0.80
#> 31 RNF130 -3.338908 2.473344e-05 5.688692e-03 0.056 0.56
#> 32 IFI30 -3.387459 6.624184e-07 1.523562e-04 0.028 0.64
#> 33 HLA-DRA -3.450292 1.268278e-08 2.917039e-06 0.417 0.92
#> 34 HLA-DQB1 -3.505836 5.620640e-06 1.292747e-03 0.028 0.56
#> 35 SERPINA1 -3.540765 1.886774e-07 4.339580e-05 0.056 0.72
#> 36 CFD -3.659355 1.963076e-06 4.515076e-04 0.056 0.64
#> 37 CST3 -3.710886 4.469249e-11 1.027927e-08 0.306 1.00
#> 38 TYMP -3.806179 1.702818e-11 3.916481e-09 0.111 1.00
#> 39 LRRC25 -3.923695 1.256935e-04 2.890952e-02 0.028 0.44
#> 40 HLA-DRB5 -4.122944 3.920170e-08 9.016391e-06 0.056 0.76
#> 41 HLA-DPA1 -4.197597 7.347202e-09 1.689856e-06 0.111 0.84
#> 42 LYZ -4.476489 6.997602e-11 1.609449e-08 0.417 1.00
#> 43 HLA-DQA1 -4.711130 1.136284e-05 2.613452e-03 0.028 0.52
#> 44 IL1B -4.725789 2.948315e-05 6.781125e-03 0.028 0.48
#> 45 MPEG1 -4.803084 1.834020e-04 4.218246e-02 0.028 0.40
#> 46 FPR1 -4.912697 2.460668e-05 5.659537e-03 0.028 0.48
#> 47 HLA-DMB -4.920761 2.145323e-05 4.934243e-03 0.028 0.48
#> 48 HLA-DRB1 -4.999548 3.287672e-10 7.561646e-08 0.083 0.88
#> 49 S100A9 -5.125239 1.542308e-09 3.547309e-07 0.194 0.88
#> 50 HLA-DPB1 -5.325399 4.061018e-10 9.340340e-08 0.083 0.88
#> 51 S100A8 -6.076803 5.334985e-11 1.227047e-08 0.111 0.96
#> 52 SMCO4 -9.369438 1.739832e-06 4.001614e-04 0.000 0.52
#> 53 C5AR1 -9.594401 1.556284e-05 3.579453e-03 0.000 0.44
#> 54 CD14 -9.883809 1.739832e-06 4.001614e-04 0.000 0.52
#> 55 MS4A6A -10.301974 1.739832e-06 4.001614e-04 0.000 0.52