Open rmalik203 opened 6 years ago
Getting same error.
Getting same error
idem
have you found a way to figure out this issue?
Manually remove the NAs from the munged sumstats file!
I would recommend loading into R and trying something like:
library(data.table) df<-fread("your_data",header=TRUE) df<-na.omit(df) write.table(df,"your_data_na_filtered",quote=FALSE,sep="\t",col.names=TRUE,row.names=FALSE)
From: polpett notifications@github.com Sent: Monday, May 4, 2020 5:09 AM To: xtonyjiang/GNOVA GNOVA@noreply.github.com Cc: Daghlas, Iyas iyas_daghlas@hms.harvard.edu; Comment comment@noreply.github.com Subject: Re: [xtonyjiang/GNOVA] Problem with NaNs (#4)
Manually remove the NAs from the munged sumstats file!
Dear daghli, dear all, I have applied a filter based on the expected ranges for each column in bash. But, how can I be sure that I have removed all the ANs from the munged sumstats file? Could you suggest a script to use for this purpose?
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I really recommend using this script, because there is no need to use R, pass parameters to it, or anything troublesome. zcat /root/ldsc/sum_use/WBC_snplist.txt.sumstats.gz | awk 'NF==5' - | gzip > /root/GNOVA/sum_use_filter_NA/WBC_snplist.txt.sumstats.gz
Hi Tony,
I've been trying to use GNOVA in my project. For some of the sumstats files I'm using, I get the following error:
I tracked it down to the prep.py, where the
df = pd.merge(bim, dfs[1], on=['SNP']).merge(dfs[0], on=['SNP'])
produces "NaN". I think this shouldn't be the case. Could this be a matter of the pandas version used? My workaround was to introduce a
df.dropna(inplace=True)
but I don't think that's how it's meant to be.
Rainer