Examples/pipeline.R

In NilsWeng/TCGAproject_repo: What the package does (short line)

#CMD
rm(list=ls())


#






library(nilsTCGA)



#Load required CNV-data from folder.Masked Copy Number Segment
setwd("C:/Users/Nils_/OneDrive/Skrivbord/R-stuff/Data")
cnv_files <- list.files(path="C:/Users/Nils_/OneDrive/Skrivbord/R-stuff/Data",recursive=TRUE,pattern="grch38.seg.v2.txt")

my_data <- lapply(cnv_files,readCNVs)



  
#names(my_data)[i] <- unique(my_data[i]$GDC_Aliquot)
  




# find all positions in all samples where segment_mean < -2
#potential_loss <- setNames(data.frame(matrix(ncol = 6, nrow = 0)), c("GDC_Aliquot","Chromosome","Start","End","Num_Probes","Segment_Mean"))


# 







# IDEA about naming the GRanges objects after their id. However what is it