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Hi,
I want to use this package to analyze my snp data. But I have a problem to create the tsv of p value.
Could you give me some advice?
Thanks in advance.
Best wishes !
Liu
The text was updated successfully, but these errors were encountered:
Hi Liu,
SNP data analysis comes with additional challenges that are not solved by
this package (many SNPs are not in genes; one gene may have multiple SNPs).
You need to solve these challenges first by assigning SNP p-values to
genes. Then make each input dataset into this format:
gene_symbol pvalue
GENE1 0.001
GENE2 0.3
GENE3 0.000006
Then in R, when you have two data.frames like that (dfr1, dfr2), you should
look at the R command merge(). Specifically, all=TRUE will merge such that
missing genes in one dataset will receive NA p-values in the other dataset.
combined_dfr = merge(dfr1, dfr2, by = "gene_symbol", all = TRUE)
I hope this helps. All the best,
Jüri
On Sat, Sep 12, 2020 at 8:50 AM tom liu ***@***.***> wrote:
Hi,
I want to use this package to analyze my snp data. But I have a problem to
create the tsv of p value.
Could you give me some advice?
Thanks in advance.
Best wishes !
Liu
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Hi,
I want to use this package to analyze my snp data. But I have a problem to create the tsv of p value.
Could you give me some advice?
Thanks in advance.
Best wishes !
Liu
The text was updated successfully, but these errors were encountered: