`no lines available in input error` while running example code
Hi!
I recently found out about your paper and very excited try your package on an ongoing project!
I was following your tutorial code and got an error.
I downloaded your master-16f2fed6ff3351cf6fcf9c1accd79fba13c5445b branch and installed to R from the source.
I was able load the VarExp library, and GWAS and COHORT data sets without any problems.
However, I am getting an error when running getGenoCorMatrix function.
Please see my code below:
> # Load the package
> library(VarExp)
> # Load the meta-analysis summary statistics file
> data(GWAS)
> head(GWAS)
RSID CHR POS A0 FREQ_A0 MAIN_EFFECT INT_EFFECT
430 rs72900467 1 989500 A 0.05558 -0.282895628 0.11487230
1085 rs34372380 1 1305201 T 0.11205 -0.003162676 0.01704444
134 rs4422949 1 834928 G 0.21753 -0.133573045 -0.11129018
469 rs9442366 1 1009234 T 0.42201 0.121852094 -0.09421119
50 rs61768199 1 781845 G 0.09736 -0.017142010 0.02977832
1318 rs9439462 1 1462766 T 0.04784 0.206595425 0.06823945
> # Load the cohort description file
> data(COHORT)
> head(COHORT)
Cohort PHENO_N PHENO_Mean PHENO_SD EXPO_Mean EXPO_SD
1 1 10000 1.297265 3.097524 2.002715 1.250979
2 2 10000 1.288332 3.152367 2.009427 1.242574
3 3 10000 1.390218 3.109720 1.995473 1.258670
4 4 10000 1.342020 3.151429 1.999943 1.256718
5 5 10000 1.385564 3.153274 2.002401 1.235129
> # Compute the genotype correlation matrix from the reference panel
> C <- getGenoCorMatrix(GWAS$RSID, GWAS$CHR, GWAS$POS, GWAS$A0, "EUR", pruning = FALSE)
Error in read.table(file = file, header = header, sep = sep, quote = quote, :
no lines available in input Am I missing something here?