Hi, 

  I am trying to use lohSpec to visualize loss of heterozygosity regions. Please find the attached code and the errors.

lohspec1a <- read.delim("C:/Users/pdharia/Desktop/GWASTools/Cluster/lohspec1a.raw")
source("https://bioconductor.org/biocLite.R")
biocLite("GenVisR")

library(GenVisR)

 lohSpec(lohspec1, path = NULL, fileExt = NULL,  y = NULL, genome = "hg19", gender = gender,  step = 1e+06, window_size = 2500000, normal = 0.5, colourScheme = "inferno", plotLayer = NULL,  method = "slide", out = "plot")

Error in lohSpec_qual(x, y, genome) : 

  Did not detect required column names in x, required columns are: chromosome position n_vaf t_vaf sample

My lohspec file has the following columns: chromosome position b_vaf t_vaf and sample. It is sorted by chromosome, position, and sample. 

I also tried writing the path instead of downloading the file in R, the code and error is as follows:

lohSpec(x= "C:/Users/pdharia/Desktop/GWASTools/Cluster/lohspec1a.txt", path = NULL, fileExt = NULL,  y = NULL, genome = "hg19", gender = NULL,  step = 1e+06, window_size = 2500000, normal = 0.5, colourScheme = "inferno", plotLayer = NULL,  method = "slide", out = "plot")

Error: $ operator is invalid for atomic vectors

Thank you for your help in advance!