Closed Chunmingl closed 1 year ago
That file should be generated when you run impute_expr_z
function. Did you run this function to impute gene z scores? Which version/branch did you use?
I did not use impute_expr_z
to impute the expression z scores, instead I used the formula in the function to compute z scores, z.g <- (t(wgt) * var.s) %*% z.s/sqrt(t(wgt) %*% Gamma.g %*% wgt)
I read that qclist
(exprqc.Rd files) was computed fromweightall <- read_weight_predictdb()
via
nwgt <- nrow(wgt.matrix) nmiss <- nrow(wgt.matrix)-length(snpnames) qclist[[gname]] <- list("n" = nwgt, "nmiss"= nmiss, "missrate"= nwgt/nmiss)
while
snpnames <- Reduce(intersect, list(rownames(wgt.matrix), ld_snpinfo$id, z_snp$id))
I wonder what are the ld_snpinfo
and z_snp
files about and what are their format requirements?
The version I am currently using is the main branch.
You can run the tutorial and it will generate .exprqc.Rd
files after you run impute_expr_z
. You can take a look at the format and generate your own exprqc.R files. The program will need to use the list variable wgtlist
stored in the .exprqc.Rd
file for downstream steps.
I am using imputed gene expression that was computed with other methods as ctwas_rss() input. I received an error message saying that
“cannot open compressed file '/(path)/....chr1.exprqc.Rd', probable reason 'No such file or directory'”.
While I have.expr
and.exprvar
files listed in the directory, would you please provide instructions about how to build.exprqc.Rd
files and the format requirement of these files?