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Question: Issues with lohSpec
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gravatar for dharia.priyadarshani
4 months ago by
dharia.priyadarshani0 wrote:

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!

 

ADD COMMENTlink written 4 months ago by dharia.priyadarshani0

From your presentation of the error message, it seems the function is expecting a column 'n_vaf' but your data has a column 'b_vaf'

ADD REPLYlink written 4 months ago by Martin Morgan ♦♦ 22k
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