Skip to content
Permalink
main
Switch branches/tags

Name already in use

A tag already exists with the provided branch name. Many Git commands accept both tag and branch names, so creating this branch may cause unexpected behavior. Are you sure you want to create this branch?
Go to file
 
 
Cannot retrieve contributors at this time
executable file 40 lines (31 sloc) 1.43 KB
##################################################
## Project: Marker Gene Definition from Allan Brain Atlas
## Date: 06.04.2020
## 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)
### HUMAN DATA #################
# Read Seurat object
data <- readRDS("allan_human/data_object_sct.rds")
# Find markers for every louvain cluster compared to all remaining cells
#data.markers <- FindAllMarkers(data, min.pct = 0.25, logfc.threshold = 0.25)
#data.markers %>% group_by(cluster) %>% top_n(n = 2, wt = avg_logFC)
#
#saveRDS(data.markers, file = "allan_human/data_markers_clusterLouvain.rds")
# Find markers for every allan cluster (141) compared to all remaining cells
Idents(data) <- "cluster_label"
ct.markers <- FindAllMarkers(data,
min.pct = 0.25,
logfc.threshold = 0.4,
only.pos = TRUE,
max.cells.per.ident = 500)
saveRDS(ct.markers, file = "allan_human/data_markers_sct_clusterAllan.rds")
# Find markers for every allan subclass (20) compared to all remaining cells
#Idents(data) <- "subclass_label"
#sc.markers <- FindAllMarkers(data,
# min.pct = 0.25,
# log.fc.threshold = 0.25)
#saveRDS(sc.markers, file = "allan_human/data_markers_subclassAllan.rds")