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LabelTransfer_SingleNuclei/02b_markerGenes_sct_integrated_pilot.R

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##################################################
## Project: Marker Genes Pilot data, SCT & Integration
## Date: 09.06.2020
## Author: Nathalie
##################################################
# setwd("/net/PE1/raid1/LAURA/SC_ANALYSIS/markerGeneDefinition")
#
# library(scrattch.io, lib.loc="pkg_r")
# library(Seurat, lib.loc="pkg_r")
# library(dplyr)
setwd("~/Documents/PostmortemBrain/analysis/markerGeneDefinition")
library(scrattch.io)
library(Seurat)
library(dplyr)
### PILOT PFC DATA #################
# Read Seurat object
data <- readRDS("pilot/data_object_sct_integrated.rds")
# Find markers for every cluster compared to all remaining cells, report only the positive ones
data.markers <- FindAllMarkers(data, min.pct = 0.25, logfc.threshold = 0.25, only.pos = TRUE)
data.markers %>% group_by(cluster) %>% top_n(n = 2, wt = avg_logFC)
saveRDS(data.markers, file = "pilot/data_markers_clusterLouvain_sct_integrated.rds")