bschilder
commented
1 year ago 1. "N"
1.a. compute_n = "ldsc" (I get sample_size=NULL: must be valid integer)
This was a bug due to me missing some places where the sample_size was still being used. I just pushed a change to contruct_colmap so that is takes the arg N= instead of sample_size. N acts just like the other mapping columns in that it renames a column based on the value supplied to the argument (construct_colmap(N="N_cases") means that the "N_cases" column will get renamed to "N" and used in any subsequent steps that require total (or effective) sample size.
Note that whenever the "N" col is present in the post-standardized sumstats data, this will be used instead of whatever you supply to compute_n. I've updated the docs to better explain this.
1.b. compute_n = data_munged$NSTUDY (This does not work at all)
This is my bad; I told you yesterday that MungeSumstats::compute_nsize(compute_n=) can take a vector of sample size. But apparently I misremembered and it can only take a single number to be applied to all rows. Instead, I'll add a line to echodata::get_sample_size that handle these scenarios:
### Numeric vector
if(is.numeric(compute_n) &&
length(compute_n)>1){
messager("Numeric vector supplied to compute_n.",v=verbose)
if(length(compute_n)!=nrow(dat2)){
stp <- paste(
"When compute_n is a numeric vector,",
"its length must be exactly equal to the number of rows",
"in your summary statistics data (dat)."
)
stop(stp)
} else {
dat2$N <- compute_n
return(dat2)
}
}2. Rfast
Rfast also wasn't installed. I've now ensured that it get automatically installed by making it an Import of echofinemap.
AMCalejandro
1. Bug description
This is the continuation of a bug description in #113. I tried to pass to finemap_loci, the munged data, and the issue with sample size keeps arising
When I pass an integer to compute_n, it sort of works assigning the same N to all SNPs. However, as you will see below, NSTUDY exists.......
2. Reproducible example
Note Reading compute_n in mungerSumStats doc, I tried....
Code
Console output
Data
Input data stored on tsv.gz file
3. Session info
(Add output of the R function
utils::sessionInfo()below. This helps us assess version/OS conflicts which could be causing bugs.)