docs/presto.md

In satijalab/seurat-wrappers: Community-Provided Methods and Extensions for the Seurat Object

Fast Differential Expression with Presto

Compiled: October 07, 2020

This vignette demonstrates the use of the Presto package in Seurat. Commands and parameters are based off of the Presto tutorial. If you use Presto in your work, please cite:

Presto scales Wilcoxon and auROC analyses to millions of observations

Ilya Korsunsky, Aparna Nathan, Nghia Millard, Soumya Raychaudhuri

bioRxiv, 2019.

Pre-print: https://www.biorxiv.org/content/10.1101/653253v1.full.pdf

GitHub: https://github.com/immunogenomics/presto

Prerequisites to install:

• Seurat
• Presto
• SeuratWrappers
• SeuratData

library(presto)
library(Seurat)
library(SeuratData)
library(SeuratWrappers)

Differential Expression Testing for PBMC scRNA-seq Data

To learn more about this dataset, type ?pbmc3k

InstallData("pbmc3k")
data("pbmc3k")
pbmc3k <- NormalizeData(pbmc3k)
Idents(pbmc3k) <- "seurat_annotations"

diffexp.B.Mono <- RunPresto(pbmc3k, "CD14+ Mono", "B")
head(diffexp.B.Mono, 10)

##                p_val avg_logFC pct.1 pct.2     p_val_adj
## CD79A  1.660326e-143 -2.989854 0.042 0.936 2.276972e-139
## TYROBP 3.516407e-138  3.512505 0.994 0.102 4.822401e-134
## S100A9 7.003189e-137  4.293303 0.996 0.134 9.604174e-133
## CST3   1.498348e-135  3.344758 0.992 0.174 2.054834e-131
## S100A4 8.872946e-135  2.854897 1.000 0.360 1.216836e-130
## LYZ    2.720838e-134  3.788514 1.000 0.422 3.731357e-130
## S100A8 3.115452e-133  4.039777 0.975 0.076 4.272530e-129
## CD79B  8.317731e-133 -2.667534 0.083 0.916 1.140694e-128
## S100A6 5.156920e-132  2.541609 0.996 0.352 7.072201e-128
## LGALS1 1.427548e-131  3.002493 0.979 0.131 1.957739e-127

diffexp.all <- RunPrestoAll(pbmc3k)
head(diffexp.all[diffexp.all$cluster == "B", ], 10)

##                     p_val avg_logFC pct.1 pct.2     p_val_adj cluster      gene
## CD79A.3      0.000000e+00  2.933865 0.936 0.044  0.000000e+00       B     CD79A
## MS4A1.3      0.000000e+00  2.290577 0.855 0.055  0.000000e+00       B     MS4A1
## LINC00926.1 2.998236e-274  1.956493 0.564 0.010 4.111781e-270       B LINC00926
## CD79B.3     1.126919e-273  2.381160 0.916 0.144 1.545457e-269       B     CD79B
## TCL1A.3     1.962618e-272  2.463556 0.622 0.023 2.691534e-268       B     TCL1A
## HLA-DQA1.2  3.017803e-267  2.104207 0.890 0.119 4.138616e-263       B  HLA-DQA1
## VPREB3      2.131575e-238  1.667466 0.488 0.008 2.923242e-234       B    VPREB3
## HLA-DQB1.2  2.076231e-230  2.112052 0.863 0.148 2.847343e-226       B  HLA-DQB1
## CD74.2      1.000691e-184  2.010688 1.000 0.819 1.372347e-180       B      CD74
## HLA-DRA.3   1.813356e-184  1.914531 1.000 0.492 2.486837e-180       B   HLA-DRA

satijalab/seurat-wrappers documentation built on April 10, 2024, 3:25 p.m.