User: dharia.priyadarshani

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Posts by dharia.priyadarshani

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Issues with lohSpec
... 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) ...
genvisr lohspec written 6 days ago by dharia.priyadarshani0
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raw text file doesn't have the expected set of SNP names
... Hi,    After getting a genotype, scan annotation, SNP annotation files from Illumina in R using GWASTools, I was checking for table(diag.geno$snp.chk). Although the SNP ID matched in geno.file and SNP annotation file  table(diag.geno$snp.chk) gives 0 for all my samples. The diag.geno gives the foll ...
snpannotation written 3 months ago by dharia.priyadarshani0
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Missing normalized x, normalized y, baf and logrrratio values
... Hi,    I am trying to load intensity files and bl files using GWASTools. I got the following error:  Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec,  :    scan() expected 'a real', got '"0.9958377"'   I checked my data and realized that my variables are a string.  1 ...
gwastools written 3 months ago by dharia.priyadarshani0 • updated 3 months ago by Stephanie M. Gogarten560
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Comment: C: Importing affymetrix genotype calls with GWASTools
... col.nums <- as.integer(c(0,1,2,3,4,5,6,7,8)); names(col.nums) <- c("Name","Chr","Position","1.B Allele Freq","1.Log R Ratio", "1.GType","2.B Allele Freq","2.Log R Ratio", "2.GType") variables = c("Name","Chr","Position","1.B Allele Freq","1.Log R Ratio", "1.GType","2.B Allele Freq","2.Log R Ra ...
written 5 months ago by dharia.priyadarshani0

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