scRNAseq_1Trimester_WTOscript

setwd("/data/scratch/anna9230")

## 09.02.2021
# script for wTO for single cell-RNA dataset 1st Trimester
library(data.table)
library(rvest)
library(wTO)
library(parallel)
library(reshape2)
library(igraph)
library(plyr)

# Load clusters
#cluster1 <- read.table("cluster1_1397genes_484cells.txt", header=TRUE, row.names=1)
#cluster2 <- read.table("cluster2_29genes_392cells.txt", header=TRUE, row.names=1)
#cluster3 <- read.table("cluster3_3Kgenes_299cells.txt", header=TRUE, row.names=1)
cluster4 <- read.table("cluster4_1kgenes_267cells.txt", header=TRUE, row.names=1)
#cluster5 <- read.table("cluster5_4Kgenes_24cells.txt", header=TRUE, row.names=1)
#cluster6 <- read.table("cluster6_645genes_20cells.txt", header=TRUE, row.names=1)
#cluster7 <- read.table("cluster7_34genes_165cells.txt", header=TRUE, row.names=1)

# load tfs and LNC
overlap <- read.csv("lnc_TF_cataloge_ready_to_use.csv",header = TRUE)


# run
wTOf_scRNA_1sttrim_cluster4new = wTO.fast( Data = cluster4, Overlap = overlap$gene.symbol, method='p',sign ="sign",delta = 0.2,
                                       n=1000, method_resampling="Bootstrap")
write.csv(wTOf_scRNA_1sttrim_cluster4new, "RES_Network_cluster4NEW_scRNA_1Trim_1000bstr.txt")