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Question: Issues with lohSpec
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gravatar for dharia.priyadarshani
10 weeks 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 10 weeks 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 10 weeks ago by Martin Morgan ♦♦ 22k
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