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KeyError: ['beta', 'SE'] when using Z #23

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opain opened this issue Jul 2, 2021 · 1 comment · May be fixed by #37
Open

KeyError: ['beta', 'SE'] when using Z #23

opain opened this issue Jul 2, 2021 · 1 comment · May be fixed by #37

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@opain
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opain commented Jul 2, 2021

Hello, Thank you for creating this method and software.

The summary statistic file format description for POPCORN suggests the output of the LDSC munge_sumstats.py script would be suitable. However, when I use LDSC munged summary statistics I receive the following error: "KeyError: ['beta', 'SE']". Is this error a result of the 'beta' and 'SE' not being present. Below is a screenshot of the log file, also showing the first ten lines of each summary statistics file.

image

Is it necessary to change the format of my summary statistics? Or is this error reflecting another issue?

Many thanks in advance.

Best wishes,

Ollie
@opain
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opain commented Sep 15, 2021

To resolve this issue I have used summary statistics that include 'beta' and 'SE' columns instead of just 'Z'. Then the analysis runs successfully.

The sumstat.py script requires beta and SE columns here, causing the error.

So, providing just the 'Z' column is not sufficient.

@opain opain closed this as completed Sep 15, 2021
@opain opain reopened this Sep 15, 2021
ofrei pushed a commit to ofrei/Popcorn that referenced this issue Oct 25, 2022
fixes brielin#23
fa1326c
@ofrei ofrei linked a pull request Oct 25, 2022 that will close this issue
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Fixes #23 KeyError: ['beta', 'SE'] when using Z ofrei/Popcorn
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@opain