I am going to analyze my own data by using Palimpsest. Befored that, I tested the installation with following command. It returned errors that seems resulted from code?
my cmd
suppressMessages(library(Palimpsest))
suppressMessages(library(BSgenome.Hsapiens.UCSC.hg19))
ref_genome <- BSgenome.Hsapiens.UCSC.hg19
#load ref data
load("Palimpsest-master/data/ensgene_hg19.RData")
load("Palimpsest-master/data/cytoband_hg19.RData")
# load rawdata
datadir <- "Palimpsest-master//RUNNING_PALIMPSEST_EXAMPLE/LiC1162"
#result DIR
resdir <- "Results";if(!file.exists(resdir)) dir.create(resdir)
#test
load(file.path(datadir,"mut_data.RData"))
load(file.path(datadir,"cna_data.RData"))
load(file.path(datadir,"annot_data.RData"))
load(file.path(datadir,"sv_data.RData"))
# Annotating the mutation data with necessary information
vcf <- preprocessInput_snv(input_data = mut_data,
ensgene = ensgene,
reference_genome = ref_genome)
I am going to analyze my own data by using Palimpsest. Befored that, I tested the installation with following command. It returned errors that seems resulted from code?
my cmd
it throw errors
Any solutions ? my session info